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US20220241320A1 - Modulators of irf4 expression - Google Patents

Modulators of irf4 expression Download PDF

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US20220241320A1
US20220241320A1 US17/554,558 US202117554558A US2022241320A1 US 20220241320 A1 US20220241320 A1 US 20220241320A1 US 202117554558 A US202117554558 A US 202117554558A US 2022241320 A1 US2022241320 A1 US 2022241320A1
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certain embodiments
compound
modified
oligonucleotide
nucleoside
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US12042510B2 (en
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Tianyuan Zhou
Youngsoo Kim
Robert MacLeod
Huynh-Hoa Bui
Susan M. Freier
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Ionis Pharmaceuticals Inc
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Ionis Pharmaceuticals Inc
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    • C12N15/113Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
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Definitions

  • the present embodiments provide methods, compounds, and compositions useful for inhibiting IRF4 expression, which can be useful for treating, preventing, or ameliorating a cancer associated with IRF4.
  • Interferon Regulatory Factor 4 is a transcription factor involved in immune responses in normal B and T cells, and is strongly implicated in the development of hematological malignancies, especially multiple mycloma (MM). High IRF4 levels is associated with a poor prognosis of overall survival for MM patients. Upregulation of the cereblon/IRF4 pathway accounts for the failure of lenalidomide treatment, an IMiD approved for MM and B cell malignancies. IRF4 is a component of super enhancer in MM cells in which a positive auto-regulatory loop between the oncogene MYC and IRF4 sustains the survival of MM.
  • IRF4 is also involved in cutaneous anaplastic large cell lymphomas DLBCL, B-cell non-Hodgkin's lymphoma, ALL, adult T cell leukemia/lymphoma (ATLL), and peripheral T cell lymphoma. Despite its role in many cancers, IRF4 is considered an undruggable target by conventional therapeutic approaches.
  • Certain embodiments provided herein are directed to potent and tolerable compounds and compositions useful for inhibiting IRF4 expression, which can be useful for treating, preventing, ameliorating, or slowing progression of cancer associated with IRF4.
  • each SEQ ID NO in the examples contained herein is independent of any modification to a sugar moiety, an internucleoside linkage, or a nucleobase.
  • compounds defined by a SEQ ID NO may comprise, independently, one or more modifications to a sugar moiety, an internucleoside linkage, or a nucleobase.
  • Compounds described by ION number indicate a combination of nucleobase sequence, chemical modification, and motif.
  • 2′-deoxynucleoside means a nucleoside comprising 2′-H(H) furanosyl sugar moiety, as found in naturally occurring deoxyribonucleic acids (DNA).
  • a 2′-deoxynucleoside may comprise a modified nucleobase or may comprise an RNA nucleobase (uracil).
  • 2′-O-methoxyethyl refers to an O-methoxy-ethyl modification at the 2′ position of a furanosyl ring.
  • a 2′-O-methoxyethyl modified sugar is a modified sugar.
  • 2′-MOE nucleoside (also 2′-O-methoxyethyl nucleoside) means a nucleoside comprising a 2′-MOE modified sugar moiety.
  • 2′-substituted nucleoside or “2-modified nucleoside” means a nucleoside comprising a 2′-substituted or 2′-modified sugar moiety.
  • “2′-substituted” or “2-modified” in reference to a sugar moiety means a sugar moiety comprising at least one 2′-substituent group other than H or OH.
  • 3′ target site refers to the nucleotide of a target nucleic acid which is complementary to the 3′-most nucleotide of a particular compound.
  • 5′ target site refers to the nucleotide of a target nucleic acid which is complementary to the 5′-most nucleotide of a particular compound.
  • 5-methylcytosine means a cytosine with a methyl group attached to the 5 position.
  • “About” means within ⁇ 10% of a value. For example, if it is stated, “the compounds affected about 70% inhibition of IRF4”, it is implied that IRF4 levels are inhibited within a range of 60% and 80%.
  • administering refers to routes of introducing a compound or composition provided herein to an individual to perform its intended function.
  • An example of a route of administration that can be used includes, but is not limited to parenteral administration, such as subcutaneous, intravenous, or intramuscular injection or infusion.
  • administering means administration of two or more compounds in any manner in which the pharmacological effects of both are manifest in the patient. Concomitant administration does not require that both compounds be administered in a single pharmaceutical composition, in the same dosage form, by the same route of administration, or at the same time. The effects of both compounds need not manifest themselves at the same time. The effects need only be overlapping for a period of time and need not be coextensive. Concomitant administration or co-administration encompasses administration in parallel or sequentially.
  • “Amelioration” refers to an improvement or lessening of at least one indicator, sign, or symptom of an associated disease, disorder, or condition.
  • amelioration includes a delay or slowing in the progression or severity of one or more indicators of a condition or disease.
  • the progression or severity of indicators may be determined by subjective or objective measures, which are known to those skilled in the art.
  • Animal refers to a human or non-human animal, including, but not limited to, mice, rats, rabbits, dogs, cats, pigs, and non-human primates, including, but not limited to, monkeys and chimpanzees.
  • Antisense activity means any detectable and/or measurable activity attributable to the hybridization of an antisense compound to its target nucleic acid.
  • antisense activity is a decrease in the amount or expression of a target nucleic acid or protein encoded by such target nucleic acid compared to target nucleic acid levels or target protein levels in the absence of the antisense compound to the target.
  • Antisense compound means a compound comprising an oligonucleotide and optionally one or more additional features, such as a conjugate group or terminal group.
  • antisense compounds include single-stranded and double-stranded compounds, such as, oligonucleotides, ribozymes, siRNAs, shRNAs, ssRNAs, and occupancy-based compounds.
  • Antisense inhibition means reduction of target nucleic acid levels in the presence of an antisense compound complementary to a target nucleic acid compared to target nucleic acid levels in the absence of the antisense compound.
  • Antisense mechanisms are all those mechanisms involving hybridization of a compound with target nucleic acid, wherein the outcome or effect of the hybridization is either target degradation or target occupancy with concomitant stalling of the cellular machinery involving, for example, transcription or splicing.
  • Antisense oligonucleotide means an oligonucleotide having a nucleobase sequence that is complementary to a target nucleic acid or region or segment thereof. In certain embodiments, an antisense oligonucleotide is specifically hybridizable to a target nucleic acid or region or segment thereof.
  • Bicyclic nucleoside or “BNA” means a nucleoside comprising a bicyclic sugar moiety.
  • “Bicyclic sugar” or “bicyclic sugar moiety” means a modified sugar moiety comprising two rings, wherein the second ring is formed via a bridge connecting two of the atoms in the first ring thereby forming a bicyclic structure.
  • the first ring of the bicyclic sugar moiety is a furanosyl moiety.
  • the bicyclic sugar moiety does not comprise a furanosyl moiety.
  • Branching group means a group of atoms having at least 3 positions that are capable of forming covalent linkages to at least 3 groups.
  • a branching group provides a plurality of reactive sites for connecting tethered ligands to an oligonucleotide via a conjugate linker and/or a cleavable moiety.
  • Cell-targeting moiety means a conjugate group or portion of a conjugate group that is capable of binding to a particular cell type or particular cell types.
  • cEt or “constrained ethyl” means a bicyclic furanosyl sugar moiety comprising a bridge connecting the 4′-carbon and the 2′-carbon, wherein the bridge has the formula: 4′-CH(CH 3 )—O-2′.
  • cEt nucleoside means a nucleoside comprising a cEt modified sugar moiety.
  • “Chemical modification” in a compound describes the substitutions or changes through chemical reaction, of any of the units in the compound relative to the original state of such unit.
  • “Modified nucleoside” means a nucleoside having, independently, a modified sugar moiety and/or modified nucleobase.
  • “Modified oligonucleotide” means an oligonucleotide comprising at least one modified internucleoside linkage, a modified sugar, and/or a modified nucleobase.
  • “Chemically distinct region” refers to a region of a compound that is in some way chemically different than another region of the same compound. For example, a region having 2′-O-methoxyethyl nucleotides is chemically distinct from a region having nucleotides without 2′-O-methoxyethyl modifications.
  • Chimeric antisense compounds means antisense compounds that have at least 2 chemically distinct regions, each position having a plurality of subunits.
  • “Chirally enriched population” mean s a plurality of molecules of identical molecular formula, wherein the number or percentage of molecules within the population that contain a particular stereochemical configuration at a particular chiral center is greater than the number or percentage of molecules expected to contain the same particular stereochemical configuration at the same particular chiral center within the population if the particular chiral center were stereorandom. Chirally enriched populations of molecules having multiple chiral centers within each molecule may contain one or more sterorandom chiral centers.
  • the molecules are modified oligonucleotides. In certain embodiments, the molecules are compounds comprising modified oligonucleotides.
  • cleavable bond means any chemical bond capable of being split.
  • a cleavable bond is selected from among: an amide, a polyamide, an ester, an ether, one or both esters of a phosphodiester, a phosphate ester, a carbamate, a di-sulfide, or a peptide.
  • “Cleavable moiety” means a bond or group of atoms that is cleaved under physiological conditions, for example, inside a cell, an animal, or a human.
  • “Complementary” in reference to an oligonucleotide means the nucleobase sequence of such oligonucleotide or one or more regions thereof matches the nucleobase sequence of another oligonucleotide or nucleic acid or one or more regions thereof when the two nucleobase sequences are aligned in opposing directions. Nucleobase matches or complementary nucleobases, as described herein, are limited to the following pairs: adenine (A) and thymine (T), adenine (A) and uracil (U), cytosine (C) and guanine (G), and 5-methyl cytosine ( m C) and guanine (G) unless otherwise specified.
  • oligonucleotides and/or nucleic acids need not have nucleobase complementarity at each nucleoside and may include one or more nucleobase mismatches.
  • “fully complementary” or “100% complementary” in reference to oligonucleotides means that such oligonucleotides have nucleobase matches at each nucleoside without any nucleobase mismatches.
  • Conjugate group means a group of atoms that is attached to an oligonucleotide. Conjugate groups include a conjugate moiety and a conjugate linker that attaches the conjugate moiety to the oligonucleotide.
  • Conjugate linker means a group of atoms comprising at least one bond that connects a conjugate moiety to an oligonucleotide.
  • Conjugate moiety means a group of atoms that is attached to an oligonucleotide via a conjugate linker.
  • Contiguous in the context of an oligonucleotide refers to nucleosides, nucleobases, sugar moieties, or internucleoside linkages that are immediately adjacent to each other.
  • contiguous nucleobases means nucleobases that are immediately adjacent to each other in a sequence.
  • Designing or “Designed to” refer to the process of designing a compound that specifically hybridizes with a selected nucleic acid molecule.
  • “Diluent” means an ingredient in a composition that lacks pharmacological activity, but is pharmaceutically necessary or desirable.
  • the diluent in an injected composition can be a liquid, e.g. saline solution.
  • “Differently modified” means chemical modifications or chemical substituents that are different from one another, including absence of modifications.
  • a MOE nucleoside and an unmodified DNA nucleoside are “differently modified,” even though the DNA nucleoside is unmodified.
  • DNA and RNA are “differently modified,” even though both are naturally-occurring unmodified nucleosides. Nucleosides that are the same but for comprising different nucleobases are not differently modified.
  • nucleoside comprising a 2′-OMe modified sugar and an unmodified adenine nucleobase and a nucleoside comprising a 2′-OMe modified sugar and an unmodified thymine nucleobase are not differently modified.
  • Dose means a specified quantity of a compound or pharmaceutical agent provided in a single administration, or in a specified time period.
  • a dose may be administered in two or more boluses, tablets, or injections.
  • the desired dose may require a volume not easily accommodated by a single injection.
  • two or more injections may be used to achieve the desired dose.
  • a dose may be administered in two or more injections to minimize injection site reaction in an individual.
  • the compound or pharmaceutical agent is administered by infusion over an extended period of time or continuously. Doses may be stated as the amount of pharmaceutical agent per hour, day, week or month.
  • Dosing regimen is a combination of doses designed to achieve one or more desired effects.
  • Double-stranded antisense compound means an antisense compound comprising two oligomeric compounds that are complementary to each other and form a duplex, and wherein one of the two said oligomeric compounds comprises an oligonucleotide.
  • Effective amount means the amount of compound sufficient to effectuate a desired physiological outcome in an individual in need of the compound.
  • the effective amount may vary among individuals depending on the health and physical condition of the individual to be treated, the taxonomic group of the individuals to be treated, the formulation of the composition, assessment of the individual's medical condition, and other relevant factors.
  • “Expression” includes all the functions by which a gene's coded information is converted into structures present and operating in a cell. Such structures include, but are not limited to, the products of transcription and translation.
  • “Gapmer” means an oligonucleotide comprising an internal region having a plurality of nucleosides that support RNase H cleavage positioned between external regions having one or more nucleosides, wherein the nucleosides comprising the internal region are chemically distinct from the nucleoside or nucleosides comprising the external regions.
  • the internal region may be referred to as the “gap” and the external regions may be referred to as the “wings.”
  • Hybridization means the annealing of oligonucleotides and/or nucleic acids. While not limited to a particular mechanism, the most common mechanism of hybridization involves hydrogen bonding, which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, between complementary nucleobases.
  • complementary nucleic acid molecules include, but are not limited to, an antisense compound and a nucleic acid target. In certain embodiments, complementary nucleic acid molecules include, but are not limited to, an oligonucleotide and a nucleic acid target.
  • “Immediately adjacent” means there are no intervening elements between the immediately adjacent elements of the same kind (e.g. no intervening nucleobases between the immediately adjacent nucleobases).
  • “Individual” means a human or non-human animal selected for treatment or therapy.
  • “Inhibiting the expression or activity” refers to a reduction or blockade of the expression or activity relative to the expression of activity in an untreated or control sample and does not necessarily indicate a total elimination of expression or activity.
  • Internucleoside linkage means a group or bond that forms a covalent linkage between adjacent nucleosides in an oligonucleotide.
  • Modified internucleoside linkage means any internucleoside linkage other than a naturally occurring, phosphate internucleoside linkage Non-phosphate linkages are referred to herein as modified internucleoside linkages.
  • Lengthened oligonucleotides are those that have one or more additional nucleosides relative to an oligonucleotide disclosed herein, e.g. a parent oligonucleotide.
  • Linked nucleosides means adjacent nucleosides linked together by an internucleoside linkage.
  • Linker-nucleoside means a nucleoside that links an oligonucleotide to a conjugate moiety. Linker-nucleosides are located within the conjugate linker of a compound. Linker-nucleosides are not considered part of the oligonucleotide portion of a compound even if they are contiguous with the oligonucleotide.
  • mismatch or “non-complementary” means a nucleobase of a first oligonucleotide that is not complementary to the corresponding nucleobase of a second oligonucleotide or target nucleic acid when the first and second oligonucleotides are aligned.
  • nucleobases including but not limited to a universal nucleobase, inosine, and hypoxanthine, are capable of hybridizing with at least one nucleobase but are still mismatched or non-complementary with respect to nucleobase to which it hybridized.
  • a nucleobase of a first oligonucleotide that is not capable of hybridizing to the corresponding nucleobase of a second oligonucleotide or target nucleic acid when the first and second oligonucleotides are aligned is a mismatch or non-complementary nucleobase.
  • Modulating refers to changing or adjusting a feature in a cell, tissue, organ or organism.
  • modulating IRF4 RNA can mean to increase or decrease the level of IRF4 RNA and/or IRF4 protein in a cell, tissue, organ or organism.
  • a “modulator” effects the change in the cell, tissue, organ or organism.
  • a IRF4 compound can be a modulator that decreases the amount of IRF4 RNA and/or IRF4 protein in a cell, tissue, organ or organism.
  • “Monomer” refers to a single unit of an oligomer. Monomers include, but are not limited to, nucleosides and nucleotides.
  • Motif means the pattern of unmodified and/or modified sugar moieties, nucleobases, and/or internucleoside linkages, in an oligonucleotide.
  • Non-bicyclic modified sugar or “non-bicyclic modified sugar moiety” means a modified sugar moiety that comprises a modification, such as a substituent, that does not form a bridge between two atoms of the sugar to form a second ring.
  • Nucleic acid refers to molecules composed of monomeric nucleotides.
  • a nucleic acid includes, but is not limited to, ribonucleic acids (RNA), deoxyribonucleic acids (DNA), single-stranded nucleic acids, and double-stranded nucleic acids.
  • Nucleobase means a heterocyclic moiety capable of pairing with a base of another nucleic acid.
  • a “naturally occurring nucleobase” is adenine (A), thymine (T), cytosine (C), uracil (U), and guanine (G).
  • a “modified nucleobase” is a naturally occurring nucleobase that is chemically modified.
  • a “universal base” or “universal nucleobase” is a nucleobase other than a naturally occurring nucleobase and modified nucleobase, and is capable of pairing with any nucleobase.
  • Nucleobase sequence means the order of contiguous nucleobases in a nucleic acid or oligonucleotide independent of any sugar or internucleoside linkage.
  • Nucleoside means a compound comprising a nucleobase and a sugar moiety. The nucleobase and sugar moiety are each, independently, unmodified or modified.
  • Modified nucleoside means a nucleoside comprising a modified nucleobase and/or a modified sugar moiety. Modified nucleosides include abasic nucleosides, which lack a nucleobase.
  • “Oligomeric compound” means a compound comprising a single oligonucleotide and optionally one or more additional features, such as a conjugate group or terminal group.
  • Oligonucleotide means a polymer of linked nucleosides each of which can be modified or unmodified, independent one from another. Unless otherwise indicated, oligonucleotides consist of 8-80 linked nucleosides. “Modified oligonucleotide” means an oligonucleotide, wherein at least one sugar, nucleobase, or internucleoside linkage is modified. “Unmodified oligonucleotide” means an oligonucleotide that does not comprise any sugar, nucleobase, or internucleoside modification.
  • Parent oligonucleotide means an oligonucleotide whose sequence is used as the basis of design for more oligonucleotides of similar sequence but with different lengths, motifs, and/or chemistries.
  • the newly designed oligonucleotides may have the same or overlapping sequence as the parent oligonucleotide.
  • Parenteral administration means administration through injection or infusion.
  • Parenteral administration includes subcutaneous administration, intravenous administration, intramuscular administration, intraarterial administration, intraperitoneal administration, or intracranial administration, e.g. intrathecal or intracerebroventricular administration.
  • “Pharmaceutically acceptable carrier or diluent” means any substance suitable for use in administering to an individual.
  • a pharmaceutically acceptable carrier can be a sterile aqueous solution, such as PBS or water-for-injection.
  • “Pharmaceutically acceptable salts” means physiologically and pharmaceutically acceptable salts of compounds, such as oligomeric compounds or oligonucleotides, i.e., salts that retain the desired biological activity of the parent compound and do not impart undesired toxicological effects thereto.
  • “Pharmaceutical agent” means a compound that provides a therapeutic benefit when administered to an individual.
  • “Pharmaceutical composition” means a mixture of substances suitable for administering to an individual.
  • a pharmaceutical composition may comprise one or more compounds or salt thereof and a sterile aqueous solution.
  • Phosphorothioate linkage means a modified phosphate linkage in which one of the non-bridging oxygen atoms is replaced with a sulfur atom.
  • a phosphorothioate internucleoside linkage is a modified internucleoside linkage.
  • Phosphorus moiety means a group of atoms comprising a phosphorus atom.
  • a phosphorus moiety comprises a mono-, di-, or tri-phosphate, or phosphorothioate.
  • “Portion” means a defined number of contiguous (i.e., linked) nucleobases of a nucleic acid. In certain embodiments, a portion is a defined number of contiguous nucleobases of a target nucleic acid. In certain embodiments, a portion is a defined number of contiguous nucleobases of an oligomeric compound.
  • Prevent refers to delaying or forestalling the onset, development or progression of a disease, disorder, or condition for a period of time from minutes to indefinitely.
  • Prodrug means a compound in a form outside the body which, when administered to an individual, is metabolized to another form within the body or cells thereof.
  • the metabolized form is the active, or more active, form of the compound (e.g., drug).
  • conversion of a prodrug within the body is facilitated by the action of an enzyme(s) (e.g., endogenous or viral enzyme) or chemical(s) present in cells or tissues, and/or by physiologic conditions.
  • Reduce means to bring down to a smaller extent, size, amount, or number.
  • RefSeq No. is a unique combination of letters and numbers assigned to a sequence to indicate the sequence is for a particular target transcript (e.g., target gene). Such sequence and information about the target gene (collectively, the gene record) can be found in a genetic sequence database. Genetic sequence databases include the NCBI Reference Sequence database, GenBank, the European Nucleotide Archive, and the DNA Data Bank of Japan (the latter three forming the International Nucleotide Sequence Database Collaboration or INSDC).
  • Regular is defined as a portion of the target nucleic acid having at least one identifiable structure, function, or characteristic.
  • RNAi compound means an antisense compound that acts, at least in part, through RISC or Ago2, but not through RNase H, to modulate a target nucleic acid and/or protein encoded by a target nucleic acid.
  • RNAi compounds include, but are not limited to double-stranded siRNA, single-stranded RNA (ssRNA), and microRNA, including microRNA mimics.
  • “Segments” are defined as smaller or sub-portions of regions within a nucleic acid.
  • Side effects means physiological disease and/or conditions attributable to a treatment other than the desired effects.
  • side effects include injection site reactions, liver function test abnormalities, renal function abnormalities, liver toxicity, renal toxicity, central nervous system abnormalities, myopathies, and malaise.
  • increased aminotransferase levels in serum may indicate liver toxicity or liver function abnormality.
  • increased bilirubin may indicate liver toxicity or liver function abnormality.
  • Single-stranded in reference to a compound means the compound has only one oligonucleotide.
  • Self-complementary means an oligonucleotide that at least partially hybridizes to itself.
  • a compound consisting of one oligonucleotide, wherein the oligonucleotide of the compound is self-complementary, is a single-stranded compound.
  • a single-stranded compound may be capable of binding to a complementary compound to form a duplex.
  • Sites are defined as unique nucleobase positions within a target nucleic acid.
  • Specifically hybridizable refers to an oligonucleotide having a sufficient degree of complementarity between the oligonucleotide and a target nucleic acid to induce a desired effect, while exhibiting minimal or no effects on non-target nucleic acids. In certain embodiments, specific hybridization occurs under physiological conditions.
  • Specifically inhibit with reference to a target nucleic acid means to reduce or block expression of the target nucleic acid while exhibiting fewer, minimal, or no effects on non-target nucleic acids. Reduction does not necessarily indicate a total elimination of the target nucleic acid's expression.
  • Standard cell assay means assay(s) described in the Examples and reasonable variations thereof.
  • Standard in vivo experiment means the procedure(s) described in the Example(s) and reasonable variations thereof.
  • “Stereorandom chiral center” in the context of a population of molecules of identical molecular formula means a chiral center having a random stereochemical configuration.
  • the number of molecules having the (S) configuration of the stereorandom chiral center may be but is not necessarily the same as the number of molecules having the (R) configuration of the stereorandom chiral center.
  • the stereochemical configuration of a chiral center is considered random when it is the result of a synthetic method that is not designed to control the stereochemical configuration.
  • a stereorandom chiral center is a stereorandom phosphorothioate internucleoside linkage.
  • “Sugar moiety” means an unmodified sugar moiety or a modified sugar moiety.
  • “Unmodified sugar moiety” or “unmodified sugar” means a 2′-OH(H) furanosyl moiety, as found in RNA (an “unmodified RNA sugar moiety”), or a 2′-H(H) moiety, as found in DNA (an “unmodified DNA sugar moiety”).
  • Unmodified sugar moieties have one hydrogen at each of the 1′, 3′, and 4′ positions, an oxygen at the 3′ position, and two hydrogens at the 5′ position.
  • “Modified sugar moiety” or “modified sugar” means a modified furanosyl sugar moiety or a sugar surrogate.
  • Modified furanosyl sugar moiety means a furanosyl sugar comprising a non-hydrogen substituent in place of at least one hydrogen of an unmodified sugar moiety.
  • a modified furanosyl sugar moiety is a 2′-substituted sugar moiety.
  • Such modified furanosyl sugar moieties include bicyclic sugars and non-bicyclic sugars.
  • “Sugar surrogate” means a modified sugar moiety having other than a furanosyl moiety that can link a nucleobase to another group, such as an internucleoside linkage, conjugate group, or terminal group in an oligonucleotide. Modified nucleosides comprising sugar surrogates can be incorporated into one or more positions within an oligonucleotide and such oligonucleotides are capable of hybridizing to complementary compounds or nucleic acids.
  • “Synergy” or “synergize” refers to an effect of a combination that is greater than additive of the effects of each component alone at the same doses.
  • IRF4 means any nucleic acid or protein of IRF4.
  • IRF4 nucleic acid means any nucleic acid encoding TRF4.
  • a TRF4 nucleic acid includes a DNA sequence encoding IRF4, an RNA sequence transcribed from DNA encoding IRF4 (including genomic DNA comprising introns and exons), and an mRNA sequence encoding IRF4.
  • IRF4 mRNA means an mRNA encoding a IRF4 protein. The target may be referred to in either upper or lower case.
  • IRF4 specific inhibitor refers to any agent capable of specifically inhibiting IRF4 RNA and/or IRF4 protein expression or activity at the molecular level.
  • IRF4 specific inhibitors include nucleic acids (including antisense compounds), peptides, antibodies, small molecules, and other agents capable of inhibiting the expression of IRF4 RNA and/or IRF4 protein.
  • Target gene refers to a gene encoding a target.
  • Targeting means the specific hybridization of a compound to a target nucleic acid in order to induce a desired effect.
  • Target nucleic acid all mean a nucleic acid capable of being targeted by compounds described herein.
  • Target region means a portion of a target nucleic acid to which one or more compounds is targeted.
  • Target segment means the sequence of nucleotides of a target nucleic acid to which a compound is targeted.
  • 5′ target site refers to the 5′-most nucleotide of a target segment.
  • 3′ target site refers to the 3′-most nucleotide of a target segment.
  • Terminal group means a chemical group or group of atoms that is covalently linked to a terminus of an oligonucleotide.
  • “Therapeutically effective amount” means an amount of a compound, pharmaceutical agent, or composition that provides a therapeutic benefit to an individual.
  • Treat refers to administering a compound or pharmaceutical composition to an animal in order to effect an alteration or improvement of a disease, disorder, or condition in the animal.
  • Certain embodiments provide methods, compounds and compositions for inhibiting IRF4 expression.
  • the IRF4 nucleic acid has the sequence set forth in RefSeq or GENBANK Accession No. NM_002460.3 or NT_034880.3_TRUNC_328000_354000 (incorporated by reference, disclosed herein as SEQ ID NO: 1 and SEQ ID NO: 2, respectively).
  • the compound is an antisense compound or oligomeric compound.
  • the compound is single-stranded. In certain embodiments, the compound is double-stranded.
  • Certain embodiments provide a compound comprising a modified oligonucleotide 8 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 8 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383.
  • the compound is an antisense compound or oligomeric compound.
  • the compound is single-stranded.
  • the compound is double-stranded.
  • the modified oligonucleotide is 10 to 30 linked nucleosides in length.
  • Certain embodiments provide a compound comprising a modified oligonucleotide 9 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 9 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383.
  • the compound is an antisense compound or oligomeric compound.
  • the compound is single-stranded.
  • the compound is double-stranded.
  • the modified oligonucleotide is 10 to 30 linked nucleosides in length.
  • Certain embodiments provide a compound comprising a modified oligonucleotide 10 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 10 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383.
  • the compound is an antisense compound or oligomeric compound.
  • the compound is single-stranded.
  • the compound is double-stranded.
  • the modified oligonucleotide is 10 to 30 linked nucleosides in length.
  • Certain embodiments provide a compound comprising a modified oligonucleotide 11 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 11 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383.
  • the compound is an antisense compound or oligomeric compound.
  • the compound is single-stranded.
  • the compound is double-stranded.
  • the modified oligonucleotide is 11 to 30 linked nucleosides in length.
  • Certain embodiments provide a compound comprising a modified oligonucleotide 12 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 12 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383.
  • the compound is an antisense compound or oligomeric compound.
  • the compound is single-stranded.
  • the compound is double-stranded.
  • the modified oligonucleotide is 12 to 30 linked nucleosides in length.
  • Certain embodiments provide a compound comprising a modified oligonucleotide 16 to 80 linked nucleosides in length and having a nucleobase sequence comprising the nucleobase sequence of any one of SEQ ID NOs: 3-3383.
  • the compound is an antisense compound or oligomeric compound.
  • the compound is single-stranded.
  • the compound is double-stranded.
  • the modified oligonucleotide is 16 to 30 linked nucleosides in length.
  • Certain embodiments provide a compound comprising a modified oligonucleotide consisting of the nucleobase sequence of any one of SEQ ID NOs: 3-3383.
  • the compound is an antisense compound or oligomeric compound.
  • the compound is single-stranded. In certain embodiments, the compound is double-stranded.
  • a compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having at least an 8, 9, 10, 11, 12, 13, 14, 15, or 16 contiguous nucleobase portion complementary to an equal length portion within the 3′UTR of SEQ ID NO: 1.
  • the 3′UTR corresponds to nucleotides 1483 to 5332 of SEQ ID NO: 1.
  • a compound comprises a modified oligonucleotide 10 to 30 linked nucleosides in length having a nucleobase sequence at least 85%, at least 90%, at least 95%, or 100% complementary across its entire length to a nucleobase sequence within the 3′UTR of SEQ ID NO: 1.
  • the 3′UTR corresponds to nucleotides 1483 to 5332 of SEQ ID NO: 1.
  • a compound comprises a modified oligonucleotide 16 to 30 linked nucleosides in length having a nucleobase sequence at least 85%, at least 90%, at least 95%, or 100% complementary across its entire length to a nucleobase sequence within the 3′UTR of SEQ ID NO: 1.
  • the 3′UTR corresponds to nucleotides 1483 to 5332 of SEQ ID NO: 1.
  • a compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having at least an 8, 9, 10, 11, 12, 13, 14, 15, or 16 contiguous nucleobase portion complementary to an equal length portion within nucleotides 4227-4244, 4227-4242, 4228-4243, or 4229-4244 of SEQ ID NO: 1.
  • the modified oligonucleotide is 10 to 30 linked nucleosides in length.
  • the modified oligonucleotide is 16 to 30 linked nucleosides in length.
  • a compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having at least an 8, 9, 10, 11, 12, 13, 14, 15, or 16 contiguous nucleobase portion complementary to an equal length portion within nucleotides 9667-9682, 11411-11426, or 18090-18105 of SEQ ID NO: 2.
  • the modified oligonucleotide is 10 to 30 linked nucleosides in length.
  • the modified oligonucleotide is 16 to 30 linked nucleosides in length.
  • a compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and complementary within nucleotides 4227-4244, 4227-4242, 4228-4243, or 4229-4244 of SEQ ID NO: 1.
  • the modified oligonucleotide is 10 to 30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 to 30 linked nucleosides in length.
  • a compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and complementary within nucleotides 9667-9682, 11411-11426, or 18090-18105 of SEQ ID NO: 2.
  • the modified oligonucleotide is 10 to 30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 to 30 linked nucleosides in length.
  • a compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least an 8, 9, 10, 11, 12, 13, 14, 15, or 16 contiguous nucleobase portion any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • the modified oligonucleotide is 10 to 30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 to 30 linked nucleosides in length.
  • a compound comprises a modified oligonucleotide 16 to 80 linked nucleosides in length and having a nucleobase sequence comprising any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • the modified oligonucleotide is 16 to 30 linked nucleosides in length.
  • a compound comprises a modified oligonucleotide 16 linked nucleosides in length having a nucleobase sequence consisting of any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • a compound targeted to IRF4 is ION 935918.
  • ION 690890, 935658, 935696, 935762, 935918, 935968, 882800, 1012795, 1014095, and 1014834 emerged as the top lead compounds.
  • ION 935918 exhibited the best combination of properties in terms of potency and tolerability out of over 3,000 compounds.
  • any of the foregoing modified oligonucleotides comprises at least one modified internucleoside linkage, at least one modified sugar, and/or at least one modified nucleobase.
  • any of the foregoing modified oligonucleotides comprises at least one modified sugar.
  • at least one modified sugar comprises a 2′-O-methoxyethyl group.
  • at least one modified sugar is a bicyclic sugar, such as a 4′-CH(CH 3 )—O-2′ group, a 4′-CH 2 —O-2′ group, or a 4′-(CH 2 ) 2 —O-2′ group.
  • the modified oligonucleotide comprises at least one modified internucleoside linkage, such as a phosphorothioate internucleoside linkage.
  • any of the foregoing modified oligonucleotides comprises at least one modified nucleobase, such as 5-methylcytosine.
  • any of the foregoing modified oligonucleotides comprises:
  • the modified oligonucleotide is 16 to 80 linked nucleosides in length having a nucleobase sequence comprising the sequence recited in any one of SEQ ID NO: 2021, 560, 559, 1330, 1540, or 3303. In certain embodiments, the modified oligonucleotide is 16 to 30 linked nucleosides in length having a nucleobase sequence comprising the sequence recited in any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • the modified oligonucleotide is 16 linked nucleosides in length having a nucleobase sequence consisting of the sequence recited in any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • a compound comprises or consists of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in any one of SEQ ID NOs: 3-3383, wherein the modified oligonucleotide comprises:
  • the gap segment is positioned between the 5′ wing segment and the 3′ wing segment and wherein each nucleoside of each wing segment comprises a modified sugar.
  • the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • a compound comprises or consists of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303, wherein the modified oligonucleotide comprises:
  • the gap segment is positioned between the 5′ wing segment and the 3′ wing segment and wherein each nucleoside of each wing segment comprises a modified sugar.
  • the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • a compound comprises or consists of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in any one of SEQ ID NOs: 1330 or 3303, wherein the modified oligonucleotide comprises:
  • a 5′ wing segment consisting of three linked nucleosides
  • a 3′ wing segment consisting of three linked nucleosides
  • the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of each wing segment comprises a cEt nucleoside; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine.
  • the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • a compound comprises or consists of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in any one of SEQ ID NOs: 559 or 560, wherein the modified oligonucleotide comprises:
  • a 3′ wing segment consisting of five linked nucleosides
  • the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein the 5′ wing segment comprises a cEt nucleoside; wherein the 3′ wing segment comprises a cEt nucleoside, a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, a 2′-O-methoxyethyl nucleoside, and a cEt nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine.
  • the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • a compound comprises or consists of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in any one of SEQ ID NOs: 1330 or 2021, wherein the modified oligonucleotide comprises:
  • a 5′ wing segment consisting of two linked nucleosides
  • a 3′ wing segment consisting of four linked nucleosides
  • the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of the 5′ wing segment comprises a cEt nucleoside; wherein the 3′ wing segment comprises a cEt nucleoside, a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, and a 2′-O-methoxyethyl nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine.
  • the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • a compound comprises or consists of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in SEQ ID NO: 560, wherein the modified oligonucleotide comprises:
  • a 5′ wing segment consisting of two linked nucleosides
  • a 3′ wing segment consisting of five linked nucleosides
  • the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of the 5′ wing segment comprises a cEt nucleoside; wherein the 3′ wing segment comprises a cEt nucleoside, a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, a 2′-O-methoxyethyl nucleoside, and a cEt nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine.
  • the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • a compound comprises or consists of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in SEQ ID NOs: 2021, wherein the modified oligonucleotide comprises:
  • a 5′ wing segment consisting of two linked nucleosides
  • a 3′ wing segment consisting of five linked nucleosides
  • the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of the 5′ wing segment comprises a cEt nucleoside; wherein the 3′ wing segment comprises a 2′-O-methoxyethyl nucleoside, a 2′-O-methoxyethyl nucleoside, a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, and a cEt nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine.
  • the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • a compound comprises or consists of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in SEQ ID NOs: 1540, wherein the modified oligonucleotide comprises:
  • a 5′ wing segment consisting of two linked nucleosides
  • a 3′ wing segment consisting of five linked nucleosides
  • the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of the 5′ wing segment comprises a cEt nucleoside; wherein the 3′ wing segment comprises a 2′-O-methoxyethyl nucleoside, a 2′-O-methoxyethyl nucleoside, a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, and a cEt nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine.
  • the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • a compound comprises or consists of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in SEQ ID NOs: 560, wherein the modified oligonucleotide comprises:
  • a 5′ wing segment consisting of two linked nucleosides
  • a 3′ wing segment consisting of five linked nucleosides
  • the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of the 5′ wing segment comprises a cEt nucleoside; wherein the 3′ wing segment comprises a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, and a 2′-O-methoxyethyl nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine.
  • the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • a compound comprises or consists of ION 935918 or salt thereof, having the following chemical structure:
  • a compound comprises or consists of the sodium salt of ION 935918, having the following chemical structure:
  • a compound comprises or consists of ION 935968 or salt thereof, having the following chemical structure:
  • a compound comprises or consists of the sodium salt of ION 935968, having the following chemical structure:
  • the compound or oligonucleotide can be at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% complementary to a nucleic acid encoding IRF4.
  • the compound can be single-stranded. In certain embodiments, the compound comprises deoxyribonucleotides. In certain embodiments, the compound is double-stranded. In certain embodiments, the compound is double-stranded and comprises ribonucleotides. In any of the foregoing embodiments, the compound can be an antisense compound or oligomeric compound.
  • the compound can be 8 to 80, 10 to 30, 12 to 50, 13 to 30, 13 to 50, 14 to 30, 14 to 50, 15 to 30, 15 to 50, 16 to 30, 16 to 50, 17 to 30, 17 to 50, 18 to 22, 18 to 24, 18 to 30, 18 to 50, 19 to 22, 19 to 30, 19 to 50, or 20 to 30 linked nucleosides in length.
  • the compound comprises or consists of an oligonucleotide.
  • compounds or compositions provided herein comprise a salt of the modified oligonucleotide.
  • the salt is a sodium salt.
  • the salt is a potassium salt.
  • the compounds or compositions as described herein are highly tolerable as demonstrated by having at least one of an increase an alanine transaminase (ALT) or aspartate transaminase (AST) value of no more than 4 fold, 3 fold, or 2 fold over saline treated animals or an increase in liver, spleen, or kidney weight of no more than 30%, 20%, 15%, 12%, 10%, 5%, or 2% compared to control treated animals.
  • the compounds or compositions as described herein are highly tolerable as demonstrated by having no increase of ALT or AST over control treated animals.
  • the compounds or compositions as described herein are highly tolerable as demonstrated by having no increase in liver, spleen, or kidney weight over control animals.
  • compositions comprising the compound of any of the aforementioned embodiments or salt thereof and at least one of a pharmaceutically acceptable carrier or diluent.
  • the composition has a viscosity less than about 40 centipoise (cP), less than about 30 centipose (cP), less than about 20 centipose (cP), less than about 15 centipose (cP), or less than about 10 centipose (cP).
  • the composition having any of the aforementioned viscosities comprises a compound provided herein at a concentration of about 100 mg/mL, about 125 mg/mL, about 150 mg/mL, about 175 mg/mL, about 200 mg/mL, about 225 mg/mL, about 250 mg/mL, about 275 mg/mL, or about 300 mg/mL.
  • the composition having any of the aforementioned viscosities and/or compound concentrations has a temperature of room temperature or about 20° C., about 21° C., about 22° C., about 23° C., about 24° C., about 25° C., about 26° C., about 27° C., about 28° C., about 29° C., or about 30° C.
  • Certain embodiments provided herein relate to methods of inhibiting IRF4 expression, which can be useful for treating, preventing, or ameliorating a cancer associated with IRF4 in an individual, by administration of a compound that targets IRF4.
  • the compound can be a IRF4 specific inhibitor.
  • the compound can be an antisense compound, oligomeric compound, or oligonucleotide targeted to IRF4.
  • cancers associated with IRF4 treatable, preventable, and/or ameliorable with the methods provided herein include blood cancer, myeloma, multiple myeloma (MM), B cell malignancies, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia.
  • the B-cell lymphoma is a non-Hodgkin's B-cell lymphoma.
  • non-Hodgkin's B-cell lymphoma of certain embodiments that can be treated with compounds provided herein include, but are not limited to, diffuse large B cell lymphoma (DLBCL), activated B-cell lymphoma (ABC-DLBCL), germinal center B-cell lymphoma (GCB DLBCL), follicular lymphoma, mucosa-associated lymphatic tissue lymphoma (MALT), small cell lymphocytic lymphoma, chronic lymphocytic leukemia, mantle cell lymphoma (MCL), Burkitt lymphoma, mediastinal large B cell lymphoma, Waldenstrom macroglobulinemia, nodal marginal zone B cell lymphoma (NMZL), splenic marginal zone lymphoma (SMZL), intravascular large B-cell lymphoma, primary effusion lymphoma, and lymphomatoid granulomatosis.
  • DLBCL diffuse large B cell lymphoma
  • the T-cell lymphoma that can be treated with compounds provided herein include, but are not limited to, peripheral T-cell lymphoma, adult T cell leukemia/lymphoma (ATLL), and anaplastic large cell lymphoma (ALCL).
  • the leukemia that can be treated with compounds provided herein includes, but is not limited to, acute lymphocytic leukemia (ALL).
  • a method of treating, preventing, or ameliorating a cancer associated with IRF4 in an individual comprises administering to the individual a compound comprising a IRF4 specific inhibitor, thereby treating, preventing, or ameliorating the cancer.
  • the compound comprises an antisense compound targeted to IRF4.
  • the compound comprises an oligonucleotide targeted to IRF4.
  • a compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 8 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383.
  • a compound comprises a modified oligonucleotide 16 to 80 linked nucleosides in length and having a nucleobase sequence comprising the nucleobase sequence of any one of SEQ ID NOs: 3-3383. In certain embodiments, a compound comprises a modified oligonucleotide consisting of the nucleobase sequence of any one of SEQ ID NOs: 3-3383. In certain embodiments, a compound comprises a modified oligonucleotide 16 to 80 linked nucleosides in length having a nucleobase sequence comprising any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • a compound comprises a modified oligonucleotide having a nucleobase sequence consisting of any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • the modified oligonucleotide can be 10 to 30 linked nucleosides in length.
  • the compound is ION 690890, 935658, 935696, 935762, 935918, 935968, 882800, 1012795, 1014095, and 1014834.
  • the compound can be single-stranded or double-stranded.
  • the compound can be an antisense compound or oligomeric compound.
  • the compound is administered to the individual parenterally. In certain embodiments, administering the compound inhibits or reduces cancer cell proliferation, tumor growth, or metastasis.
  • a method of treating or ameliorating caner comprises administering to the individual a compound comprising a IRF4 specific inhibitor, thereby treating or ameliorating the cancer.
  • the cancer is a blood cancer, myeloma, multiple myeloma (MM), B cell malignancy, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia.
  • the B-cell lymphoma is a non-Hodgkin's B-cell lymphoma.
  • non-Hodgkin's B-cell lymphoma of certain embodiments that can be treated with compounds provided herein include, but are not limited to, diffuse large B cell lymphoma (DLBCL), activated B-cell lymphoma (ABC-DLBCL), germinal center B-cell lymphoma (GCB DLBCL), follicular lymphoma, mucosa-associated lymphatic tissue lymphoma (MALT), small cell lymphocytic lymphoma, chronic lymphocytic leukemia, mantle cell lymphoma (MCL), Burkitt lymphoma, mediastinal large B cell lymphoma, Waldenström macroglobulinemia, nodal marginal zone B cell lymphoma (NMZL), splenic marginal zone lymphoma (SMZL), intravascular large B-cell lymphoma, primary effusion lymphoma, and lymphomatoid granulomatosis.
  • DLBCL diffuse large B cell lymphoma
  • the T-cell lymphoma that can be treated with compounds provided herein include, but are not limited to, peripheral T-cell lymphoma, adult T cell leukemia/lymphoma (ATLL), and anaplastic large cell lymphoma (ALCL).
  • the leukemia that can be treated with compounds provided herein includes, but is not limited to, acute lymphocytic leukemia (ALL).
  • ALL acute lymphocytic leukemia
  • the compound comprises an antisense compound targeted to IRF4.
  • the compound comprises an oligonucleotide targeted to IRF4.
  • the compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 8 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383.
  • the compound comprises a modified oligonucleotide 16 to 80 linked nucleosides in length and having a nucleobase sequence comprising the nucleobase sequence of any one of SEQ ID NOs: 3-3383.
  • the compound comprises a modified oligonucleotide consisting of the nucleobase sequence of any one of SEQ ID NOs: 3-3383.
  • the compound comprises a modified oligonucleotide of 16 to 80 linked nucleosides in length having a nucleobase sequence comprising any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • the compound comprises a modified oligonucleotide having a nucleobase sequence consisting of any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • the modified oligonucleotide can be 10 to 30 linked nucleosides in length.
  • the compound is ION 690890, 935658, 935696, 935762, 935918, 935968, 882800, 1012795, 1014095, and 1014834.
  • the compound can be single-stranded or double-stranded.
  • the compound can be an antisense compound or oligomeric compound.
  • the compound is administered to the individual parenterally. In certain embodiments, administering the compound inhibits or reduces cancer cell proliferation, tumor growth, or metastasis. In certain embodiments, the individual is identified as having or at risk of having a cancer associated with IRF4.
  • a method of inhibiting expression of IRF4 in an individual having, or at risk of having, a cancer associated with IRF4 comprises administering to the individual a compound comprising a IRF4 specific inhibitor, thereby inhibiting expression of IRF4 in the individual.
  • administering the compound inhibits expression of IRF4 in the bone marrow, lymphoid tissue, or lymph node.
  • the individual has, or is at risk of having blood cancer, myeloma, multiple myeloma (MM), B cell malignancies, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia.
  • the B-cell lymphoma is a non-Hodgkin's B-cell lymphoma.
  • non-Hodgkin's B-cell lymphoma of certain embodiments that can be treated with compounds provided herein include, but are not limited to, diffuse large B cell lymphoma (DLBCL), activated B-cell lymphoma (ABC-DLBCL), germinal center B-cell lymphoma (GCB DLBCL), follicular lymphoma, mucosa-associated lymphatic tissue lymphoma (MALT), small cell lymphocytic lymphoma, chronic lymphocytic leukemia, mantle cell lymphoma (MCL), Burkitt lymphoma, mediastinal large B cell lymphoma, Waldenstrom macroglobulinemia, nodal marginal zone B cell lymphoma (NMZL), splenic marginal zone lymphoma (SMZL), intravascular large B-cell lymphoma, primary effusion lymphoma, and lymphomatoid granulomatosis.
  • DLBCL diffuse large B cell lymphoma
  • the T-cell lymphoma that can be treated with compounds provided herein include, but are not limited to, peripheral T-cell lymphoma, adult T cell leukemia/lymphoma (ATLL), and anaplastic large cell lymphoma (ALCL).
  • the leukemia that can be treated with compounds provided herein includes, but is not limited to, acute lymphocytic leukemia (ALL).
  • ALL acute lymphocytic leukemia
  • the compound comprises an antisense compound targeted to IRF4.
  • the compound comprises an oligonucleotide targeted to IRF4.
  • the compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 8 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383.
  • the compound comprises a modified oligonucleotide 16 to 80 linked nucleosides in length and having a nucleobase sequence comprising the nucleobase sequence of any one of SEQ ID NOs: 3-3383.
  • the compound comprises a modified oligonucleotide consisting of the nucleobase sequence of any one of SEQ ID NOs: 3-3383.
  • the compound comprises a modified oligonucleotide of 16 to 80 linked nucleosides in length having a nucleobase sequence comprising any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • the compound comprises a modified oligonucleotide having a nucleobase sequence consisting of any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • the modified oligonucleotide can be 10 to 30 linked nucleosides in length.
  • the compound is ION 690890, 935658, 935696, 935762, 935918, 935968, 882800, 1012795, 1014095, and 1014834.
  • the compound can be single-stranded or double-stranded.
  • the compound can be an antisense compound or oligomeric compound.
  • the compound is administered to the individual parenterally. In certain embodiments, administering the compound inhibits or reduces cancer cell proliferation, tumor growth, or metastasis. In certain embodiments, the individual is identified as having or at risk of having a cancer associated with IRF4.
  • a method of inhibiting expression of IRF4 in a cell comprises contacting the cell with a compound comprising a IRF4 specific inhibitor, thereby inhibiting expression of IRF4 in the cell.
  • the cell is a cancer cell.
  • the cell is a bone marrow, lymphoid tissue, or lymph node cell.
  • the cell is in the bone marrow, lymphoid tissue, or lymph node.
  • the cell is in the bone marrow, lymphoid tissue, or lymph node of an individual who has, or is at risk of having cancer, such as blood cancer, myeloma, multiple myeloma (MM), B cell malignancies, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia.
  • the compound comprises an antisense compound targeted to IRF4.
  • the compound comprises an oligonucleotide targeted to IRF4.
  • the compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 8 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383.
  • the compound comprises a modified oligonucleotide 16 to 80 linked nucleosides in length and having a nucleobase sequence comprising the nucleobase sequence of any one of SEQ ID NOs: 3-3383.
  • the compound comprises a modified oligonucleotide consisting of the nucleobase sequence of any one of SEQ ID NOs: 3-3383.
  • the compound comprises a modified oligonucleotide of 16 to 80 linked nucleosides in length having a nucleobase sequence comprising any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • the compound comprises a modified oligonucleotide having a nucleobase sequence consisting of any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • the modified oligonucleotide can be 10 to 30 linked nucleosides in length.
  • the compound is ION 690890, 935658, 935696, 935762, 935918, 935968, 882800, 1012795, 1014095, and 1014834.
  • the compound can be single-stranded or double-stranded.
  • the compound can be an antisense compound or oligomeric compound.
  • a method of reducing or inhibiting cancer cell proliferation, tumor growth, or metastasis of an individual having, or at risk of having, a cancer associated with IRF4 comprises administering to the individual a compound comprising a IRF4 specific inhibitor, thereby reducing or inhibiting cancer cell proliferation, tumor growth, or metastasis in the individual.
  • the individual has, or is at risk of having, blood cancer, myeloma, multiple myeloma (MM), B cell malignancies, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia.
  • cancers associated with IRF4 treatable, preventable, and/or ameliorable with the methods provided herein include blood cancer, myeloma, multiple myeloma (MM), B cell malignancies, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia.
  • the B-cell lymphoma is a non-Hodgkin's B-cell lymphoma.
  • non-Hodgkin's B-cell lymphoma of certain embodiments that can be treated with compounds provided herein include, but are not limited to, diffuse large B cell lymphoma (DLBCL), activated B-cell lymphoma (ABC-DLBCL), germinal center B-cell lymphoma (GCB DLBCL), follicular lymphoma, mucosa-associated lymphatic tissue lymphoma (MALT), small cell lymphocytic lymphoma, chronic lymphocytic leukemia, mantle cell lymphoma (MCL), Burkitt lymphoma, mediastinal large B cell lymphoma, Waldenstrom macroglobulinemia, nodal marginal zone B cell lymphoma (NMZL), splenic marginal zone lymphoma (SMZL), intravascular large B-cell lymphoma, primary effusion lymphoma, and lymphomatoid granulomatosis.
  • DLBCL diffuse large B cell lymphoma
  • the T-cell lymphoma that can be treated with compounds provided herein include, but are not limited to, peripheral T-cell lymphoma, adult T cell leukemia/lymphoma (ATLL), and anaplastic large cell lymphoma (ALCL).
  • the leukemia that can be treated with compounds provided herein includes, but is not limited to, acute lymphocytic leukemia (ALL).
  • ALL acute lymphocytic leukemia
  • the compound comprises an antisense compound targeted to IRF4.
  • the compound comprises an oligonucleotide targeted to IRF4.
  • the compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 8 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383.
  • the compound comprises a modified oligonucleotide 16 to 80 linked nucleosides in length and having a nucleobase sequence comprising the nucleobase sequence of any one of SEQ ID NOs: 3-3383.
  • the compound comprises a modified oligonucleotide consisting of the nucleobase sequence of any one of SEQ ID NOs: 3-3383.
  • the compound comprises a modified oligonucleotide of 16 to 80 linked nucleosides in length having a nucleobase sequence comprising any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • the compound comprises a modified oligonucleotide having a nucleobase sequence consisting of any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • the modified oligonucleotide can be 10 to 30 linked nucleosides in length.
  • the compound is ION 690890, 935658, 935696, 935762, 935918, 935968, 882800, 1012795, 1014095, and 1014834.
  • the compound can be single-stranded or double-stranded.
  • the compound can be an antisense compound or oligomeric compound.
  • the compound is administered to the individual parenterally. In certain embodiments, the individual is identified as having or at risk of having a cancer associated with IRF4.
  • the cancer is a blood cancer, myeloma, multiple myeloma (MM), B cell malignancy, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia.
  • the B-cell lymphoma is a non-Hodgkin's B-cell lymphoma.
  • non-Hodgkin's B-cell lymphoma of certain embodiments that can be treated with compounds provided herein include, but are not limited to, diffuse large B cell lymphoma (DLBCL), activated B-cell lymphoma (ABC-DLBCL), germinal center B-cell lymphoma (GCB DLBCL), follicular lymphoma, mucosa-associated lymphatic tissue lymphoma (MALT), small cell lymphocytic lymphoma, chronic lymphocytic leukemia, mantle cell lymphoma (MCL), Burkitt lymphoma, mediastinal large B cell lymphoma, Waldenstrom macroglobulinemia, nodal marginal zone B cell lymphoma (NMZL), splenic marginal zone lymphoma (SMZL), intravascular large B-cell lymphoma, primary effusion lymphoma, and lymphomatoid granulomatosis.
  • DLBCL diffuse large B cell lymphoma
  • the T-cell lymphoma that can be treated with compounds provided herein include, but are not limited to, peripheral T-cell lymphoma, adult T cell leukemia/lymphoma (ATLL), and anaplastic large cell lymphoma (ALCL).
  • the leukemia that can be treated with compounds provided herein includes, but is not limited to, acute lymphocytic leukemia (ALL).
  • ALL acute lymphocytic leukemia
  • the compound comprises an antisense compound targeted to IRF4.
  • the compound comprises an oligonucleotide targeted to IRF4.
  • the compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 8 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383.
  • the compound comprises a modified oligonucleotide 16 to 80 linked nucleosides in length and having a nucleobase sequence comprising the nucleobase sequence of any one of SEQ ID NOs: 3-3383.
  • the compound comprises a modified oligonucleotide consisting of the nucleobase sequence of any one of SEQ ID NOs: 3-3383.
  • the compound comprises a modified oligonucleotide of 16 to 80 linked nucleosides in length having a nucleobase sequence comprising any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • the compound comprises a modified oligonucleotide having a nucleobase sequence consisting of any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • the modified oligonucleotide can be 10 to 30 linked nucleosides in length.
  • the compound is ION 690890, 935658, 935696, 935762, 935918, 935968, 882800, 1012795, 1014095, and 1014834.
  • the compound can be single-stranded or double-stranded.
  • the compound can be an antisense compound or oligomeric compound.
  • Certain embodiments are drawn to a compound comprising a IRF4 specific inhibitor for use in reducing or inhibiting cancer cell proliferation, tumor growth, or metastasis in an individual having cancer.
  • the cancer is a blood cancer, myeloma, multiple myeloma (MM), B cell malignancy, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia.
  • the compound comprises an antisense compound targeted to IRF4.
  • the compound comprises an oligonucleotide targeted to IRF4.
  • the compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 8 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383.
  • the compound comprises a modified oligonucleotide 16 to 80 linked nucleosides in length and having a nucleobase sequence comprising the nucleobase sequence of any one of SEQ ID NOs: 3-3383.
  • the compound comprises a modified oligonucleotide consisting of the nucleobase sequence of any one of SEQ ID NOs: 3-3383.
  • the compound comprises a modified oligonucleotide of 16 to 80 linked nucleosides in length having a nucleobase sequence comprising any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • the compound comprises a modified oligonucleotide having a nucleobase sequence consisting of any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • the modified oligonucleotide can be 10 to 30 linked nucleosides in length.
  • the compound is ION 690890, 935658, 935696, 935762, 935918, 935968, 882800, 1012795, 1014095, and 1014834.
  • the compound can be single-stranded or double-stranded.
  • the compound can be an antisense compound or oligomeric compound.
  • Certain embodiments are drawn to use of a compound comprising a IRF4 specific inhibitor for the manufacture or preparation of a medicament for treating cancer. Certain embodiments are drawn to use of a compound comprising a IRF4 specific inhibitor for the preparation of a medicament for treating a cancer associated with IRF4.
  • the cancer is a blood cancer, myeloma, multiple myeloma (MM), B cell malignancy, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia.
  • the B-cell lymphoma is a non-Hodgkin's B-cell lymphoma.
  • non-Hodgkin's B-cell lymphoma of certain embodiments that can be treated with compounds provided herein include, but are not limited to, diffuse large B cell lymphoma (DLBCL), activated B-cell lymphoma (ABC-DLBCL), germinal center B-cell lymphoma (GCB DLBCL), follicular lymphoma, mucosa-associated lymphatic tissue lymphoma (MALT), small cell lymphocytic lymphoma, chronic lymphocytic leukemia, mantle cell lymphoma (MCL), Burkitt lymphoma, mediastinal large B cell lymphoma, Waldenström macroglobulinemia, nodal marginal zone B cell lymphoma (NMZL), splenic marginal zone lymphoma (SMZL), intravascular large B-cell lymphoma, primary effusion lymphoma, and lymphomatoid granulomatosis.
  • DLBCL diffuse large B cell lymphoma
  • the T-cell lymphoma that can be treated with compounds provided herein include, but are not limited to, peripheral T-cell lymphoma, adult T cell leukemia/lymphoma (ATLL), and anaplastic large cell lymphoma (ALCL).
  • the leukemia that can be treated with compounds provided herein includes, but is not limited to, acute lymphocytic leukemia (ALL).
  • ALL acute lymphocytic leukemia
  • the compound comprises an antisense compound targeted to IRF4.
  • the compound comprises an oligonucleotide targeted to IRF4.
  • the compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 8 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383.
  • the compound comprises a modified oligonucleotide 16 to 80 linked nucleosides in length and having a nucleobase sequence comprising the nucleobase sequence of any one of SEQ ID NOs: 3-3383.
  • the compound comprises a modified oligonucleotide consisting of the nucleobase sequence of any one of SEQ ID NOs: 3-3383.
  • the compound comprises a modified oligonucleotide of 16 to 80 linked nucleosides in length having a nucleobase sequence comprising any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • the compound comprises a modified oligonucleotide having a nucleobase sequence consisting of any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • the modified oligonucleotide can be 10 to 30 linked nucleosides in length.
  • the compound is ION 690890, 935658, 935696, 935762, 935918, 935968, 882800, 1012795, 1014095, and 1014834.
  • the compound can be single-stranded or double-stranded.
  • the compound can be an antisense compound or oligomeric compound.
  • Certain embodiments are drawn to use of a compound comprising a IRF4 specific inhibitor for the manufacture or preparation of a medicament for reducing or inhibiting cancer cell proliferation, tumor growth, or metastasis in an individual having cancer.
  • the cancer is a blood cancer, myeloma, multiple myeloma (MM), B cell malignancy, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia.
  • Certain embodiments are drawn to use of a compound comprising a TRF4 specific inhibitor for the preparation of a medicament for reducing or inhibiting cancer cell proliferation, tumor growth, or metastasis in an individual having cancer.
  • the cancer is a blood cancer, myeloma, multiple myeloma (MM), B cell malignancy, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia.
  • the B-cell lymphoma is a non-Hodgkin's B-cell lymphoma.
  • non-Hodgkin's B-cell lymphoma examples include, but are not limited to, diffuse large B cell lymphoma (DLBCL), activated B-cell lymphoma (ABC-DLBCL), germinal center B-cell lymphoma (GCB DLBCL), follicular lymphoma, mucosa-associated lymphatic tissue lymphoma (MALT), small cell lymphocytic lymphoma, chronic lymphocytic leukemia, mantle cell lymphoma (MCL), Burkitt lymphoma, mediastinal large B cell lymphoma, Waldenström macroglobulinemia, nodal marginal zone B cell lymphoma (NMZL), splenic marginal zone lymphoma (SMZL), intravascular large B-cell lymphoma, primary effusion lymphoma, and lymphomatoid granulomatosis.
  • DLBCL germinal center B-cell lymphoma
  • MALT mucosa-associated lymphatic tissue lymphoma
  • the T-cell lymphoma includes, but is not limited to, peripheral T-cell lymphoma, adult T cell leukemia/lymphoma (ATLL), and anaplastic large cell lymphoma (ALCL).
  • the leukemia includes, but is not limited to, acute lymphocytic leukemia (ALL).
  • the compound comprises an antisense compound targeted to TRF4.
  • the compound comprises an oligonucleotide targeted to IRF4.
  • the compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 8 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383.
  • the compound comprises a modified oligonucleotide 16 to 80 linked nucleosides in length and having a nucleobase sequence comprising the nucleobase sequence of any one of SEQ ID NOs: 3-3383.
  • the compound comprises a modified oligonucleotide consisting of the nucleobase sequence of any one of SEQ ID NOs: 3-3383.
  • the compound comprises a modified oligonucleotide of 16 to 80 linked nucleosides in length having a nucleobase sequence comprising any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • the compound comprises a modified oligonucleotide having a nucleobase sequence consisting of any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • the modified oligonucleotide can be 10 to 30 linked nucleosides in length.
  • the compound is ION 690890, 935658, 935696, 935762, 935918, 935968, 882800, 1012795, 1014095, and 1014834.
  • the compound can be single-stranded or double-stranded.
  • the compound can be an antisense compound or oligomeric compound.
  • the compound can be targeted to IRF4.
  • the compound comprises or consists of a modified oligonucleotide, for example a modified oligonucleotide 8 to 80 linked nucleosides in length, 10 to 30 linked nucleosides in length, 12 to 30 linked nucleosides in length, or 20 linked nucleosides in length.
  • the modified oligonucleotide is at least 80%, 85%, 90%, 95% or 100% complementary to any of the nucleobase sequences recited in SEQ ID NOs: 1-2.
  • the modified oligonucleotide comprises at least one modified internucleoside linkage, at least one modified sugar and/or at least one modified nucleobase.
  • the modified internucleoside linkage is a phosphorothioate internucleoside linkage
  • the modified sugar is a bicyclic sugar or a 2′-O-methoxyethyl
  • the modified nucleobase is a 5-methylcytosine.
  • the modified oligonucleotide comprises a gap segment consisting of linked deoxynucleosides; a 5′ wing segment consisting of linked nucleosides; and a 3′ wing segment consisting of linked nucleosides, wherein the gap segment is positioned immediately adjacent to and between the 5′ wing segment and the 3′ wing segment and wherein each nucleoside of each wing segment comprises a modified sugar.
  • the modified oligonucleotide can be 12 to 30, 15 to 30, 15 to 25, 15 to 24, 16 to 24, 17 to 24, 18 to 24, 19 to 24, 20 to 24, 19 to 22, 20 to 22, 16 to 20, or 17 or 20 linked nucleosides in length.
  • the modified oligonucleotide is at least 80%, 85%, 90%, 95% or 100% complementary to any of the nucleobase sequences recited in SEQ ID NOs: 1-2.
  • the modified oligonucleotide comprises at least one modified internucleoside linkage, at least one modified sugar and/or at least one modified nucleobase.
  • the modified internucleoside linkage is a phosphorothioate internucleoside linkage
  • the modified sugar is a bicyclic sugar or a 2′-O-methoxyethyl
  • the modified nucleobase is a 5-methylcytosine.
  • the modified oligonucleotide comprises a gap segment consisting of linked 2′-deoxynucleosides; a 5′ wing segment consisting of linked nucleosides; and a 3′ wing segment consisting of linked nucleosides, wherein the gap segment is positioned immediately adjacent to and between the 5′ wing segment and the 3′ wing segment and wherein each nucleoside of each wing segment comprises a modified sugar.
  • the compound can comprise or consist of a modified oligonucleotide 16 to 80 linked nucleosides in length and having a nucleobase sequence comprising any one of SEQ ID NOs: 3-3383, wherein the modified oligonucleotide comprises:
  • the gap segment is positioned between the 5′ wing segment and the 3′ wing segment and wherein each nucleoside of each wing segment comprises a modified sugar.
  • the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • the compound can comprise or consist of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303, wherein the modified oligonucleotide comprises:
  • the gap segment is positioned between the 5′ wing segment and the 3′ wing segment and wherein each nucleoside of each wing segment comprises a modified sugar.
  • the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • the compound can comprise or consist of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in any one of SEQ ID NOs: 1330 or 3303, wherein the modified oligonucleotide comprises:
  • a 5′ wing segment consisting of three linked nucleosides
  • a 3′ wing segment consisting of three linked nucleosides
  • the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of each wing segment comprises a cEt nucleoside; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine.
  • the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • the compound can comprise or consist of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in any one of SEQ ID NOs: 559 or 560, wherein the modified oligonucleotide comprises:
  • a 3′ wing segment consisting of five linked nucleosides
  • the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein the 5′ wing segment comprises a cEt nucleoside; wherein the 3′ wing segment comprises a cEt nucleoside, a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, a 2′-O-methoxyethyl nucleoside, and a cEt nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine.
  • the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • the compound can comprise or consist of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in any one of SEQ ID NOs: 1330 or 2021, wherein the modified oligonucleotide comprises:
  • a 5′ wing segment consisting of two linked nucleosides
  • a 3′ wing segment consisting of four linked nucleosides
  • the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of the 5′ wing segment comprises a cEt nucleoside; wherein the 3′ wing segment comprises a cEt nucleoside, a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, and a 2′-O-methoxyethyl nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine.
  • the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • the compound can comprise or consist of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in SEQ ID NO: 560, wherein the modified oligonucleotide comprises:
  • a 5′ wing segment consisting of two linked nucleosides
  • a 3′ wing segment consisting of five linked nucleosides
  • the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of the 5′ wing segment comprises a cEt nucleoside; wherein the 3′ wing segment comprises a cEt nucleoside, a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, a 2′-O-methoxyethyl nucleoside, and a cEt nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine.
  • the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • the compound can comprise or consist of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in SEQ ID NOs: 2021, wherein the modified oligonucleotide comprises:
  • a 5′ wing segment consisting of two linked nucleosides
  • a 3′ wing segment consisting of five linked nucleosides
  • the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of the 5′ wing segment comprises a cEt nucleoside; wherein the 3′ wing segment comprises a 2′-O-methoxyethyl nucleoside, a 2′-O-methoxyethyl nucleoside, a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, and a cEt nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine.
  • the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • the compound can comprise or consist of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in SEQ ID NOs: 1540, wherein the modified oligonucleotide comprises:
  • a 5′ wing segment consisting of two linked nucleosides
  • a 3′ wing segment consisting of five linked nucleosides
  • the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of the 5′ wing segment comprises a cEt nucleoside; wherein the 3′ wing segment comprises a 2′-O-methoxyethyl nucleoside, a 2′-O-methoxyethyl nucleoside, a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, and a cEt nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine.
  • the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • the compound can comprise or consist of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in SEQ ID NOs: 560, wherein the modified oligonucleotide comprises:
  • a 5′ wing segment consisting of two linked nucleosides
  • a 3′ wing segment consisting of five linked nucleosides
  • the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of the 5′ wing segment comprises a cEt nucleoside; wherein the 3′ wing segment comprises a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, and a 2′-O-methoxyethyl nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine.
  • the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • the compound can comprise or consist of ION 935918 or salt thereof, having the following chemical structure:
  • the compound can comprise or consist of the sodium salt of ION 935918, having the following chemical structure:
  • the compound can comprise or consist of ION 935968 or salt thereof, having the following chemical structure:
  • the compound can comprise or consist of the sodium salt of ION 935968, having the following chemical structure:
  • the compound can be administered parenterally.
  • parenteral administration includes subcutaneous administration, intravenous administration, intramuscular administration, intraarterial administration, intraperitoneal administration, or intracranial administration, e.g. intrathecal or intracerebroventricular administration.
  • a first agent comprising a compound described herein is co-administered with one or more secondary agents.
  • such second agents are designed to treat the same disease, disorder, or condition as the first agent described herein.
  • such second agents are designed to treat a different disease, disorder, or condition as the first agent described herein.
  • a first agent is designed to treat an undesired side effect of a second agent.
  • second agents are co-administered with the first agent to treat an undesired effect of the first agent.
  • such second agents are designed to treat an undesired side effect of one or more pharmaceutical compositions as described herein.
  • second agents are co-administered with the first agent to produce a combinational effect. In certain embodiments, second agents are co-administered with the first agent to produce a synergistic effect. In certain embodiments, the co-administration of the first and second agents permits use of lower dosages than would be required to achieve a therapeutic or prophylactic effect if the agents were administered as independent therapy.
  • one or more compounds or compositions provided herein are co-administered with one or more secondary agents. In certain embodiments, one or more compounds or compositions provided herein and one or more secondary agents, are administered at different times. In certain embodiments, one or more compounds or compositions provided herein and one or more secondary agents, are prepared together in a single formulation. In certain embodiments, one or more compounds or compositions provided herein and one or more secondary agents, are prepared separately.
  • a secondary agent is selected from: proteasome inhibitors including but not limited to bortezomib, carfilzomib, and ixazomib; BTK inhibitors including but not limited to ibrutinib; IMiDs including but not limited to thalidomide, lenalidomide, and pomalidomide; BCL2 inhibitors including but not limited to venetoclax; HDAC inhibitors including but not limited to panobinostat; CDK inhibitors including but not limited to dinaciclib; XPO1 inhibitors including but not limited to selinexor; BET inhibitors including but not limited to CPI-0610; anti-CD38 antibodies including but not limited to daratumumab, isatuximab, and MOR202; anti-CD319 or anti-SLAMF7 antibodies including but not limited to elotuzumab; dexamethasone, cisplatin, doxorubicin, cyclophosphamide, and
  • Certain embodiments are directed to the use of a compound targeted to IRF4 as described herein in combination with a secondary agent.
  • such use is in a method of treating a patient suffering from cancer including, but not limited to, blood cancer, myeloma, multiple myeloma (MM), B cell malignancies, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia.
  • such use is in the preparation or manufacture of a medicament for treating cancer including, but not limited to, blood cancer, myeloma, multiple myeloma (MM), B cell malignancies, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia.
  • the B-cell lymphoma is a non-Hodgkin's B-cell lymphoma.
  • non-Hodgkin's B-cell lymphoma of certain embodiments that can be treated with compounds provided herein include, but are not limited to, diffuse large B cell lymphoma (DLBCL), activated B-cell lymphoma (ABC-DLBCL), germinal center B-cell lymphoma (GCB DLBCL), follicular lymphoma, mucosa-associated lymphatic tissue lymphoma (MALT), small cell lymphocytic lymphoma, chronic lymphocytic leukemia, mantle cell lymphoma (MCL), Burkitt lymphoma, mediastinal large B cell lymphoma, Waldenström macroglobulinemia, nodal marginal zone B cell lymphoma (NMZL), splenic marginal zone lymphoma (SMZL), intravascular large B-cell lymphoma, primary effusion lymphoma
  • the T-cell lymphoma includes, but is not limited to, peripheral T-cell lymphoma, adult T cell leukemia/lymphoma (ATLL), and anaplastic large cell lymphoma (ALCL).
  • the leukemia includes, but is not limited to, acute lymphocytic leukemia (ALL).
  • a secondary agent is selected from: proteasome inhibitors including but not limited to bortezomib, carfilzomib, and ixazomib; BTK inhibitors including but not limited to ibrutinib; IMiDs including but not limited to thalidomide, lenalidomide, and pomalidomide; BCL2 inhibitors including but not limited to venetoclax; HDAC inhibitors including but not limited to panobinostat; CDK inhibitors including but not limited to dinaciclib; XPO1 inhibitors including but not limited to selinexor; BET inhibitors including but not limited to CPI-0610; anti-CD38 antibodies including but not limited to daratumumab, isatuximab, and MOR202; anti-CD319 or anti-SLAMF7 antibodies including but not limited to elotuzumab; dexamethasone, cisplatin, doxorubicin, cyclophosphamide, and
  • Certain embodiments are drawn to a combination of a compound targeted to IRF4 as described herein and a secondary agent, such as a secondary agent selected from: proteasome inhibitors including but not limited to bortezomib, carfilzomib, and ixazomib; BTK inhibitors including but not limited to ibrutinib; IMiDs including but not limited to thalidomide, lenalidomide, and pomalidomide; BCL2 inhibitors including but not limited to venetoclax; HDAC inhibitors including but not limited to panobinostat; CDK inhibitors including but not limited to dinaciclib; XPO1 inhibitors including but not limited to selinexor; BET inhibitors including but not limited to CPI-0610; dexamethasone, thalidomide, cisplatin, doxorubicin, cyclophosphamide, and etoposide.
  • a secondary agent such as a secondary agent selected from: proteasome inhibitor
  • such a combination of a compound targeted to IRF4 as described herein and a secondary agent such as a secondary agent selected from: proteasome inhibitors including but not limited to bortezomib, carfilzomib, and ixazomib; BTK inhibitors including but not limited to ibrutinib; IMiDs including but not limited to lenalidomide; BCL2 inhibitors including but not limited to venetoclax; HDAC inhibitors including but not limited to panobinostat; CDK inhibitors including but not limited to dinaciclib; XPO1 inhibitors including but not limited to selinexor; BET inhibitors including but not limited to CPI-0610; anti-CD38 antibodies including but not limited to daratumumab, isatuximab, and MOR202; anti-CD319 or anti-SLAMF7 antibodies including but not limited to elotuzumab; dexamethasone, cisplatin, doxorubicin,
  • Such combinations can be useful for reducing or inhibiting cancer cell proliferation, tumor growth, or metastasis and/or treating cancer including, but not limited to, blood cancer, mycloma, multiple mycloma (MM), B cell malignancies, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia.
  • mycloma multiple mycloma
  • MM multiple mycloma
  • B cell malignancies lymphoma
  • B cell lymphoma B cell lymphoma
  • T cell lymphoma T cell lymphoma
  • leukemia leukemia
  • the compound targeted to IRF4 as described herein and the secondary agent are used in combination treatment by administering the two agents simultaneously, separately or sequentially.
  • the two agents are formulated as a fixed dose combination product.
  • the two agents are provided to the patient as separate units which can then either be taken simultaneously or serially (sequentially).
  • compounds described herein can be antisense compounds.
  • the antisense compound comprises or consists of an oligomeric compound.
  • the oligomeric compound comprises a modified oligonucleotide.
  • the modified oligonucleotide has a nucleobase sequence complementary to that of a target nucleic acid.
  • a compound described herein comprises or consists of a modified oligonucleotide.
  • the modified oligonucleotide has a nucleobase sequence complementary to that of a target nucleic acid.
  • a compound or antisense compound is single-stranded.
  • Such a single-stranded compound or antisense compound comprises or consists of an oligomeric compound.
  • such an oligomeric compound comprises or consists of an oligonucleotide and optionally a conjugate group.
  • the oligonucleotide is an antisense oligonucleotide.
  • the oligonucleotide is modified.
  • the oligonucleotide of a single-stranded antisense compound or oligomeric compound comprises a self-complementary nucleobase sequence.
  • compounds are double-stranded.
  • Such double-stranded compounds comprise a first modified oligonucleotide having a region complementary to a target nucleic acid and a second modified oligonucleotide having a region complementary to the first modified oligonucleotide.
  • the modified oligonucleotide is an RNA oligonucleotide.
  • the thymine nucleobase in the modified oligonucleotide is replaced by a uracil nucleobase.
  • compound comprises a conjugate group.
  • one of the modified oligonucleotides is conjugated.
  • both the modified oligonucleotides are conjugated.
  • the first modified oligonucleotide is conjugated.
  • the second modified oligonucleotide is conjugated.
  • the first modified oligonucleotide is 12-30 linked nucleosides in length and the second modified oligonucleotide is 12-30 linked nucleosides in length.
  • one of the modified oligonucleotides has a nucleobase sequence comprising at least 8 contiguous nucleobases of any of SEQ ID NOs: 3-3383.
  • antisense compounds are double-stranded.
  • Such double-stranded antisense compounds comprise a first oligomeric compound having a region complementary to a target nucleic acid and a second oligomeric compound having a region complementary to the first oligomeric compound.
  • the first oligomeric compound of such double stranded antisense compounds typically comprises or consists of a modified oligonucleotide and optionally a conjugate group.
  • the oligonucleotide of the second oligomeric compound of such double-stranded antisense compound may be modified or unmodified. Either or both oligomeric compounds of a double-stranded antisense compound may comprise a conjugate group.
  • the oligomeric compounds of double-stranded antisense compounds may include non-complementary overhanging nucleosides.
  • single-stranded and double-stranded compounds include but are not limited to oligonucleotides, siRNAs, microRNA targeting oligonucleotides, and single-stranded RNAi compounds, such as small hairpin RNAs (shRNAs), single-stranded siRNAs (ssRNAs), and microRNA mimics.
  • shRNAs small hairpin RNAs
  • ssRNAs single-stranded siRNAs
  • microRNA mimics microRNA mimics.
  • a compound described herein has a nucleobase sequence that, when written in the 5′ to 3′ direction, comprises the reverse complement of the target segment of a target nucleic acid to which it is targeted.
  • a compound described herein comprises an oligonucleotide 10 to 30 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 12 to 30 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 12 to 22 linked subunits in length. In certain embodiments, compound described herein comprises an oligonucleotide 14 to 30 linked subunits in length. In certain embodiments, compound described herein comprises an oligonucleotide 14 to 20 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 15 to 30 linked subunits in length.
  • a compound described herein comprises an oligonucleotide 15 to 20 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 16 to 30 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 16 to 20 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 17 to 30 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 17 to 20 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 18 to 30 linked subunits in length.
  • a compound described herein comprises an oligonucleotide 18 to 21 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 18 to 20 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 20 to 30 linked subunits in length.
  • oligonucleotides are 12 to 30 linked subunits, 14 to 30 linked subunits, 14 to 20 subunits, 15 to 30 subunits, 15 to 20 subunits, 16 to 30 subunits, 16 to 20 subunits, 17 to 30 subunits, 17 to 20 subunits, 18 to 30 subunits, 18 to 20 subunits, 18 to 21 subunits, 20 to 30 subunits, or 12 to 22 linked subunits in length, respectively.
  • a compound described herein comprises an oligonucleotide 14 linked subunits in length.
  • a compound described herein comprises an oligonucleotide 16 linked subunits in length.
  • a compound described herein comprises an oligonucleotide 17 linked subunits in length. In certain embodiments, compound described herein comprises an oligonucleotide 18 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 19 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 20 linked subunits in length.
  • a compound described herein comprises an oligonucleotide 8 to 80, 12 to 50, 13 to 30, 13 to 50, 14 to 30, 14 to 50, 15 to 30, 15 to 50, 16 to 30, 16 to 50, 17 to 30, 17 to 50, 18 to 22, 18 to 24, 18 to 30, 18 to 50, 19 to 22, 19 to 30, 19 to 50, or 20 to 30 linked subunits.
  • the compound described herein comprises an oligonucleotide 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, or 80 linked subunits in length, or a range defined by any two of the above values.
  • the linked subunits are nucleotides, nucleosides, or nucleobases.
  • the compound may further comprise additional features or elements, such as a conjugate group, that are attached to the oligonucleotide.
  • a conjugate group comprises a nucleoside (i.e. a nucleoside that links the conjugate group to the oligonucleotide)
  • the nucleoside of the conjugate group is not counted in the length of the oligonucleotide.
  • compounds may be shortened or truncated.
  • a single subunit may be deleted from the 5′ end (5′ truncation), or alternatively from the 3′ end (3′ truncation).
  • a shortened or truncated compound targeted to an IRF4 nucleic acid may have two subunits deleted from the 5′ end, or alternatively may have two subunits deleted from the 3′ end, of the compound.
  • the deleted nucleosides may be dispersed throughout the compound.
  • the additional subunit When a single additional subunit is present in a lengthened compound, the additional subunit may be located at the 5′ or 3′ end of the compound. When two or more additional subunits are present, the added subunits may be adjacent to each other, for example, in a compound having two subunits added to the 5′ end (5′ addition), or alternatively to the 3′ end (3′ addition), of the compound. Alternatively, the added subunits may be dispersed throughout the compound.
  • RNAi interfering RNA compounds
  • siRNA double-stranded RNA compounds
  • ssRNA single-stranded RNAi compounds
  • siRNA is meant to be equivalent to other terms used to describe nucleic acid molecules that are capable of mediating sequence specific RNAi, for example short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), short hairpin RNA (shRNA), short interfering oligonucleotide, short interfering nucleic acid, short interfering modified oligonucleotide, chemically modified siRNA, post-transcriptional gene silencing RNA (ptgsRNA), and others.
  • RNAi is meant to be equivalent to other terms used to describe sequence specific RNA interference, such as post transcriptional gene silencing, translational inhibition, or epigenetics.
  • a compound described herein can comprise any of the oligonucleotide sequences targeted to IRF4 described herein.
  • the compound can be double-stranded.
  • the compound comprises a first strand comprising at least an 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 contiguous nucleobase portion of any one of SEQ ID NOs: 3-3383 and a second strand.
  • the compound comprises a first strand comprising the nucleobase sequence of any one of SEQ ID NOs: 3-3383 and a second strand.
  • the compound comprises ribonucleotides in which the first strand has uracil (U) in place of thymine (T) in any one of SEQ ID NOs: 3-3383.
  • the compound comprises (i) a first strand comprising a nucleobase sequence complementary to the site on IRF4 to which any of SEQ ID NOs: 3-3383 is targeted, and (ii) a second strand.
  • the compound comprises one or more modified nucleotides in which the 2′ position in the sugar contains a halogen (such as fluorine group; 2′-F) or contains an alkoxy group (such as a methoxy group; 2′-OMe).
  • the compound comprises at least one 2′-F sugar modification and at least one 2′-OMe sugar modification.
  • the at least one 2′-F sugar modification and at least one 2′-OMe sugar modification are arranged in an alternating pattern for at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 contiguous nucleobases along a strand of the dsRNA compound.
  • the compound comprises one or more linkages between adjacent nucleotides other than a naturally-occurring phosphodiester linkage Examples of such linkages include phosphoramide, phosphorothioate, and phosphorodithioate linkages.
  • the compounds may also be chemically modified nucleic acid molecules as taught in U.S. Pat. No. 6,673,661.
  • the compound contains one or two capped strands, as disclosed, for example, by WO 00/63364, filed Apr. 19, 2000.
  • the first strand of the compound is an siRNA guide strand and the second strand of the compound is an siRNA passenger strand.
  • the second strand of the compound is complementary to the first strand.
  • each strand of the compound is 16, 17, 18, 19, 20, 21, 22, or 23 linked nucleosides in length.
  • the first or second strand of the compound can comprise a conjugate group.
  • a compound described herein can comprise any of the oligonucleotide sequences targeted to IRF4 described herein.
  • the compound is single stranded.
  • such a compound is a single-stranded RNAi (ssRNAi) compound.
  • the compound comprises at least an 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 contiguous nucleobase portion of any one of SEQ ID NOs: 3-3383.
  • the compound comprises the nucleobase sequence of any one of SEQ ID NOs: 3-3383.
  • the compound comprises ribonucleotides in which uracil (U) is in place of thymine (T) in any one of SEQ ID NOs: 3-3383.
  • the compound comprises a nucleobase sequence complementary to the site on IRF4 to which any of SEQ ID NOs: 3-3383 is targeted.
  • the compound comprises one or more modified nucleotides in which the 2′ position in the sugar contains a halogen (such as fluorine group; 2′-F) or contains an alkoxy group (such as a methoxy group; 2′-OMe).
  • the compound comprises at least one 2′-F sugar modification and at least one 2′-OMe sugar modification.
  • the at least one 2′-F sugar modification and at least one 2′-OMe sugar modification are arranged in an alternating pattern for at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 contiguous nucleobases along a strand of the compound.
  • the compound comprises one or more linkages between adjacent nucleotides other than a naturally-occurring phosphodiester linkage. Examples of such linkages include phosphoramide, phosphorothioate, and phosphorodithioate linkages.
  • the compounds may also be chemically modified nucleic acid molecules as taught in U.S. Pat. No. 6,673,661.
  • the compound contains a capped strand, as disclosed, for example, by WO 00/63364, filed Apr. 19, 2000.
  • the compound consists of 16, 17, 18, 19, 20, 21, 22, or 23 linked nucleosides.
  • the compound can comprise a conjugate group.
  • compounds described herein comprise modified oligonucleotides.
  • Certain modified oligonucleotides have one or more asymmetric center and thus give rise to enantiomers, diastereomers, and other stereoisomeric configurations that may be defined, in terms of absolute stereochemistry, as (R) or (S), as ⁇ or ⁇ such as for sugar anomers, or as (D) or (L) such as for amino acids etc.
  • Included in the modified oligonucleotides provided herein are all such possible isomers, including their racemic and optically pure forms, unless specified otherwise. Likewise, all cis- and trans-isomers and tautomeric forms are also included.
  • the compounds described herein include variations in which one or more atoms are replaced with a non-radioactive isotope or radioactive isotope of the indicated element.
  • compounds herein that comprise hydrogen atoms encompass all possible deuterium substitutions for each of the 1 H hydrogen atoms.
  • Isotopic substitutions encompassed by the compounds herein include but are not limited to: 2 H or 3 H in place of 1 H, 13 C or 14 C in place of 12 C, 15 N in place of 14 N, 17 O or 18 O in place of 16 O, and 33 S, 34 S, 35 S, or 36 S in place of 32 S.
  • non-radioactive isotopic substitutions may impart new properties on the compound that are beneficial for use as a therapeutic or research tool.
  • radioactive isotopic substitutions may make the compound suitable for research or diagnostic purposes, such as an imaging assay.
  • compounds described herein comprise or consist of modified oligonucleotides. In certain embodiments, compounds described herein are antisense compounds. In certain embodiments, compounds comprise oligomeric compounds. In certain embodiments, compounds described herein are capable of hybridizing to a target nucleic acid, resulting in at least one antisense activity. In certain embodiments, compounds described herein selectively affect one or more target nucleic acid.
  • Such compounds comprise a nucleobase sequence that hybridizes to one or more target nucleic acid, resulting in one or more desired antisense activity and does not hybridize to one or more non-target nucleic acid or does not hybridize to one or more non-target nucleic acid in such a way that results in a significant undesired antisense activity.
  • hybridization of a compound described herein to a target nucleic acid results in recruitment of a protein that cleaves the target nucleic acid.
  • certain compounds described herein result in RNase H mediated cleavage of the target nucleic acid.
  • RNase H is a cellular endonuclease that cleaves the RNA strand of an RNA:DNA duplex.
  • the DNA in such an RNA:DNA duplex need not be unmodified DNA.
  • compounds described herein are sufficiently “DNA-like” to elicit RNase H activity. Further, in certain embodiments, one or more non-DNA-like nucleoside in the gap of a gapmer is tolerated.
  • RNA-induced silencing complex RISC
  • compounds described herein or a portion of the compound is loaded into an RNA-induced silencing complex (RISC), ultimately resulting in cleavage of the target nucleic acid.
  • RISC RNA-induced silencing complex
  • certain compounds described herein result in cleavage of the target nucleic acid by Argonaute.
  • Compounds that are loaded into RISC are RNAi compounds.
  • RNAi compounds may be double-stranded (siRNA) or single-stranded (ssRNA).
  • hybridization of compounds described herein to a target nucleic acid does not result in recruitment of a protein that cleaves that target nucleic acid. In certain such embodiments, hybridization of the compound to the target nucleic acid results in alteration of splicing of the target nucleic acid. In certain embodiments, hybridization of the compound to a target nucleic acid results in inhibition of a binding interaction between the target nucleic acid and a protein or other nucleic acid. In certain such embodiments, hybridization of the compound to a target nucleic acid results in alteration of translation of the target nucleic acid.
  • Antisense activities may be observed directly or indirectly.
  • observation or detection of an antisense activity involves observation or detection of a change in an amount of a target nucleic acid or protein encoded by such target nucleic acid, a change in the ratio of splice variants of a nucleic acid or protein, and/or a phenotypic change in a cell or animal.
  • compounds described herein comprise or consist of an oligonucleotide comprising a region that is complementary to a target nucleic acid.
  • the target nucleic acid is an endogenous RNA molecule.
  • the target nucleic acid encodes a protein.
  • the target nucleic acid is selected from: an mRNA and a pre-mRNA, including intronic, exonic and untranslated regions.
  • the target RNA is an mRNA.
  • the target nucleic acid is a pre-mRNA.
  • the target region is entirely within an intron.
  • the target region spans an intron/exon junction.
  • the target region is at least 50% within an intron.
  • Nucleotide sequences that encode IRF4 include, without limitation, the following: RefSEQ No. NM_002460.3 and NT_034880.3_TRUNC_328000_354000.
  • hybridization occurs between a compound disclosed herein and a IRF4 nucleic acid.
  • the most common mechanism of hybridization involves hydrogen bonding (e.g., Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding) between complementary nucleobases of the nucleic acid molecules.
  • Hybridization can occur under varying conditions. Hybridization conditions are sequence-dependent and are determined by the nature and composition of the nucleic acid molecules to be hybridized.
  • the compounds provided herein are specifically hybridizable with a IRF4 nucleic acid.
  • An oligonucleotide is said to be complementary to another nucleic acid when the nucleobase sequence of such oligonucleotide or one or more regions thereof matches the nucleobase sequence of another oligonucleotide or nucleic acid or one or more regions thereof when the two nucleobase sequences are aligned in opposing directions.
  • Nucleobase matches or complementary nucleobases, as described herein, are limited to the following pairs: adenine (A) and thymine (T), adenine (A) and uracil (U), cytosine (C) and guanine (G), and 5-methyl cytosine (mC) and guanine (G) unless otherwise specified.
  • Complementary oligonucleotides and/or nucleic acids need not have nucleobase complementarity at each nucleoside and may include one or more nucleobase mismatches.
  • An oligonucleotide is fully complementary or 100% complementary when such oligonucleotides have nucleobase matches at each nucleoside without any nucleobase mismatches.
  • compounds described herein comprise or consist of modified oligonucleotides. In certain embodiments, compounds described herein are antisense compounds. In certain embodiments, compounds comprise oligomeric compounds. Non-complementary nucleobases between a compound and a IRF4 nucleic acid may be tolerated provided that the compound remains able to specifically hybridize to a target nucleic acid. Moreover, a compound may hybridize over one or more segments of a IRF4 nucleic acid such that intervening or adjacent segments are not involved in the hybridization event (e.g., a loop structure, mismatch or hairpin structure).
  • the compounds provided herein, or a specified portion thereof are, are at least, or are up to 70%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% complementary to a IRF4 nucleic acid, a target region, target segment, or specified portion thereof.
  • the compounds provided herein, or a specified portion thereof are 70% to 75%, 75% to 80%, 80% to 85%, 85% to 90%, 90% to 95%, 95% to 100%, or any number in between these ranges, complementary to a IRF4 nucleic acid, a target region, target segment, or specified portion thereof. Percent complementarity of a compound with a target nucleic acid can be determined using routine methods.
  • a compound in which 18 of 20 nucleobases of the compound are complementary to a target region, and would therefore specifically hybridize would represent 90 percent complementarity.
  • the remaining non-complementary nucleobases may be clustered or interspersed with complementary nucleobases and need not be contiguous to each other or to complementary nucleobases.
  • a compound which is 18 nucleobases in length having four non-complementary nucleobases which are flanked by two regions of complete complementarity with the target nucleic acid would have 77.8% overall complementarity with the target nucleic acid.
  • Percent complementarity of a compound with a region of a target nucleic acid can be determined routinely using BLAST programs (basic local alignment search tools) and PowerBLAST programs known in the art (Altschul et al., J. Mol. Biol., 1990, 215, 403 410; Zhang and Madden, Genome Res., 1997, 7, 649 656). Percent homology, sequence identity or complementarity, can be determined by, for example, the Gap program (Wisconsin Sequence Analysis Package, Version 8 for Unix, Genetics Computer Group, University Research Park, Madison Wis.), using default settings, which uses the algorithm of Smith and Waterman (Adv. Appl. Math., 1981, 2, 482 489).
  • compounds described herein, or specified portions thereof are fully complementary (i.e. 100% complementary) to a target nucleic acid, or specified portion thereof.
  • a compound may be fully complementary to a IRF4 nucleic acid, or a target region, or a target segment or target sequence thereof.
  • “fully complementary” means each nucleobase of a compound is complementary to the corresponding nucleobase of a target nucleic acid.
  • a 20 nucleobase compound is fully complementary to a target sequence that is 400 nucleobases long, so long as there is a corresponding 20 nucleobase portion of the target nucleic acid that is fully complementary to the compound.
  • Fully complementary can also be used in reference to a specified portion of the first and/or the second nucleic acid.
  • a 20 nucleobase portion of a 30 nucleobase compound can be “fully complementary” to a target sequence that is 400 nucleobases long.
  • the 20 nucleobase portion of the 30 nucleobase compound is fully complementary to the target sequence if the target sequence has a corresponding 20 nucleobase portion wherein each nucleobase is complementary to the 20 nucleobase portion of the compound.
  • the entire 30 nucleobase compound may or may not be fully complementary to the target sequence, depending on whether the remaining 10 nucleobases of the compound are also complementary to the target sequence.
  • compounds described herein comprise one or more mismatched nucleobases relative to the target nucleic acid.
  • antisense activity against the target is reduced by such mismatch, but activity against a non-target is reduced by a greater amount.
  • selectivity of the compound is improved.
  • the mismatch is specifically positioned within an oligonucleotide having a gapmer motif. In certain such embodiments, the mismatch is at position 1, 2, 3, 4, 5, 6, 7, or 8 from the 5′-end of the gap region. In certain such embodiments, the mismatch is at position 9, 8, 7, 6, 5, 4, 3, 2, 1 from the 3′-end of the gap region.
  • the mismatch is at position 1, 2, 3, or 4 from the 5′-end of the wing region. In certain such embodiments, the mismatch is at position 4, 3, 2, or 1 from the 3′-end of the wing region. In certain embodiments, the mismatch is specifically positioned within an oligonucleotide not having a gapmer motif. In certain such embodiments, the mismatch is at position 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 from the 5′-end of the oligonucleotide. In certain such embodiments, the mismatch is at position, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 from the 3′-end of the oligonucleotide.
  • non-complementary nucleobase may be at the 5′ end or 3′ end of the compound.
  • the non-complementary nucleobase or nucleobases may be at an internal position of the compound.
  • two or more non-complementary nucleobases may be contiguous (i.e. linked) or non-contiguous.
  • a non-complementary nucleobase is located in the wing segment of a gapmer oligonucleotide.
  • compounds described herein that are, or are up to 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleobases in length comprise no more than 4, no more than 3, no more than 2, or no more than 1 non-complementary nucleobase(s) relative to a target nucleic acid, such as a IRF4 nucleic acid, or specified portion thereof.
  • compounds described herein that are, or are up to 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleobases in length comprise no more than 6, no more than 5, no more than 4, no more than 3, no more than 2, or no more than 1 non-complementary nucleobase(s) relative to a target nucleic acid, such as a IRF4 nucleic acid, or specified portion thereof.
  • compounds described herein also include those which are complementary to a portion of a target nucleic acid.
  • portion refers to a defined number of contiguous (i.e. linked) nucleobases within a region or segment of a target nucleic acid.
  • a “portion” can also refer to a defined number of contiguous nucleobases of a compound.
  • the—compounds are complementary to at least an 8 nucleobase portion of a target segment.
  • the compounds are complementary to at least a 9 nucleobase portion of a target segment.
  • the compounds are complementary to at least a 10 nucleobase portion of a target segment.
  • the compounds are complementary to at least an 11 nucleobase portion of a target segment. In certain embodiments, the compounds are complementary to at least a 12 nucleobase portion of a target segment. In certain embodiments, the compounds are complementary to at least a 13 nucleobase portion of a target segment. In certain embodiments, the compounds are complementary to at least a 14 nucleobase portion of a target segment. In certain embodiments, the compounds are complementary to at least a 15 nucleobase portion of a target segment. In certain embodiments, the compounds are complementary to at least a 16 nucleobase portion of a target segment. Also contemplated are compounds that are complementary to at least a 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more nucleobase portion of a target segment, or a range defined by any two of these values.
  • the compounds provided herein may also have a defined percent identity to a particular nucleotide sequence, SEQ ID NO, or compound represented by a specific ION number, or portion thereof.
  • compounds described herein are antisense compounds or oligomeric compounds.
  • compounds described herein are modified oligonucleotides.
  • a compound is identical to the sequence disclosed herein if it has the same nucleobase pairing ability. For example, a RNA which contains uracil in place of thymidine in a disclosed DNA sequence would be considered identical to the DNA sequence since both uracil and thymidine pair with adenine.
  • Non-identical bases may be adjacent to each other or dispersed throughout the compound. Percent identity of an compound is calculated according to the number of bases that have identical base pairing relative to the sequence to which it is being compared.
  • compounds described herein, or portions thereof are, or are at least, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to one or more of the compounds or SEQ ID NOs, or a portion thereof, disclosed herein.
  • compounds described herein are about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, or any percentage between such values, to a particular nucleotide sequence, SEQ ID NO, or compound represented by a specific ION number, or portion thereof, in which the compounds comprise an oligonucleotide having one or more mismatched nucleobases.
  • the mismatch is at position 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 from the 5′-end of the oligonucleotide.
  • the mismatch is at position, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 from the 3′-end of the oligonucleotide.
  • compounds described herein comprise or consist of antisense compounds.
  • a portion of the antisense compound is compared to an equal length portion of the target nucleic acid.
  • an 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleobase portion is compared to an equal length portion of the target nucleic acid.
  • compounds described herein comprise or consist of oligonucleotides.
  • a portion of the oligonucleotide is compared to an equal length portion of the target nucleic acid.
  • an 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleobase portion is compared to an equal length portion of the target nucleic acid.
  • compounds described herein comprise or consist of oligonucleotides consisting of linked nucleosides.
  • Oligonucleotides may be unmodified oligonucleotides (RNA or DNA) or may be modified oligonucleotides.
  • Modified oligonucleotides comprise at least one modification relative to unmodified RNA or DNA (i.e., comprise at least one modified nucleoside (comprising a modified sugar moiety and/or a modified nucleobase) and/or at least one modified internucleoside linkage).
  • Modified nucleosides comprise a modified sugar moiety or a modified nucleobase or both a modified sugar moiety and a modified nucleobase.
  • sugar moieties are non-bicyclic modified sugar moieties.
  • modified sugar moieties are bicyclic or tricyclic sugar moieties.
  • modified sugar moieties are sugar surrogates. Such sugar surrogates may comprise one or more substitutions corresponding to those of other types of modified sugar moieties.
  • modified sugar moieties are non-bicyclic modified sugar moieties comprising a furanosyl ring with one or more acyclic substituent, including but not limited to substituents at the 2′, 4′, and/or 5′ positions.
  • one or more acyclic substituent of non-bicyclic modified sugar moieties is branched.
  • 2′-substituent groups suitable for non-bicyclic modified sugar moieties include but are not limited to: 2′-F, 2′-OCH 3 (“OMe” or “O-methyl”), and 2′-O(CH 2 ) 2 OCH 3 (“MOE”).
  • 2′-substituent groups are selected from among: halo, allyl, amino, azido, SH, CN, OCN, CF 3 , OCF 3 , O—C 1 -C 10 alkoxy, O—C 1 -C 10 substituted alkoxy, O—C 1 -C 10 alkyl, O—C 1 -C 10 substituted alkyl, S-alkyl, N(R m )-alkyl, O-alkenyl, S-alkenyl, N(R m )-alkenyl, O-alkynyl, S-alkynyl, N(R m )-alkynyl, O-alkylenyl-O-alkyl, alkynyl, alkaryl, aralkyl, O-alkaryl, O-aralkyl, O(CH 2 ) 2 SCH 3 , O(CH 2 ) 2 O N(R m )(R n )
  • these 2′-substituent groups can be further substituted with one or more substituent groups independently selected from among: hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro (NO 2 ), thiol, thioalkoxy, thioalkyl, halogen, alkyl, aryl, alkenyl and alkynyl.
  • Examples of 4′-substituent groups suitable for linearly non-bicyclic modified sugar moieties include but are not limited to alkoxy (e.g., methoxy), alkyl, and those described in Manoharan et al., WO 2015/106128.
  • Examples of 5′-substituent groups suitable for non-bicyclic modified sugar moieties include but are not limited to: 5′-methyl (R or S), 5′-vinyl, and 5′-methoxy.
  • non-bicyclic modified sugars comprise more than one non-bridging sugar substituent, for example, 2′-F-5′-methyl sugar moieties and the modified sugar moieties and modified nucleosides described in Migawa et al., US2010/190837 and Rajeev et al., US2013/0203836.
  • a 2′-substituted nucleoside or 2′-non-bicyclic modified nucleoside comprises a sugar moiety comprising a linear 2′-substituent group selected from: F, NH 2 , N 3 , OCF 3 , OCH 3 , O(CH 2 ) 3 NH 2 , CH 2 CH ⁇ CH 2 , OCH 2 CH ⁇ CH 2 , OCH 2 CH 2 OCH 3 , O(CH 2 ) 2 SCH 3 , O(CH 2 ) 2 ON(R m )(R n ), O(CH 2 ) 2 O(CH 2 ) 2 N(CH 3 ) 2 , and N-substituted acetamide (OCH 2 C( ⁇ O)—N(R m )(R n )), where each R m and R n is, independently, H, an amino protecting group, or substituted or unsubstituted C 1 -C 10 alkyl.
  • a 2′-substituted nucleoside or 2′-non-bicyclic modified nucleoside comprises a sugar moiety comprising a linear 2′-substituent group selected from: F, OCF 3 , OCH 3 , OCH 2 CH 2 OCH 3 , O(CH 2 ) 2 SCH 3 , O(CH 2 ) 2 ON(CH 3 ) 2 , O(CH 2 ) 2 O(CH 2 ) 2 N(CH 3 ) 2 , and OCH 2 C( ⁇ O)—N(H)CH 3 (“NMA”).
  • a linear 2′-substituent group selected from: F, OCF 3 , OCH 3 , OCH 2 CH 2 OCH 3 , O(CH 2 ) 2 SCH 3 , O(CH 2 ) 2 ON(CH 3 ) 2 , O(CH 2 ) 2 O(CH 2 ) 2 N(CH 3 ) 2 , and OCH 2 C( ⁇ O)—N(H)CH 3 (“N
  • a 2′-substituted nucleoside or 2′-non-bicyclic modified nucleoside comprises a sugar moiety comprising a linear 2′-substituent group selected from: F, OCH 3 , and OCH 2 CH 2 OCH 3 .
  • Nucleosides comprising modified sugar moieties are referred to by the position(s) of the substitution(s) on the sugar moiety of the nucleoside.
  • nucleosides comprising 2′-substituted or 2-modified sugar moieties are referred to as 2′-substituted nucleosides or 2-modified nucleosides.
  • modified sugar moieties comprise a bridging sugar substituent that forms a second ring resulting in a bicyclic sugar moiety.
  • the bicyclic sugar moiety comprises a bridge between the 4′ and the 2′ furanose ring atoms.
  • 4′ to 2′ bridging sugar substituents include but are not limited to: 4′-CH 2 -2′, 4′-(CH 2 ) 2 -2′, 4′-(CH 2 ) 3 -2′, (“LNA”), 4′-CH 2 —S-2′, 4′-(CH 2 ) 2 —O-2′ (“ENA”), 4′-CH(CH 3 )—O-2′ (referred to as “constrained ethyl” or “cEt” when in the S configuration), 4′-CH 2 —O—CH 2 -2′, 4′-CH 2 —N(R)-2′, 4′-CH(CH 2 OCH 3 )—O-2′ (“constrained MOE” or “cMOE”) and analogs thereof (see, e.g., Seth et al., U.S.
  • each R, R a , and R b is, independently, H, a protecting group, or C 1 -C 12 alkyl (see, e.g. Imanishi et al., U.S. Pat. No. 7,427,672).
  • such 4′ to 2′ bridges independently comprise from 1 to 4 linked groups independently selected from: — ⁇ C(R a )(R b ) ⁇ n —, — ⁇ C(R a )(R b ) ⁇ n —O—, —C(R a ) ⁇ C(R b )—, —C(R a ) ⁇ N—, —C( ⁇ NR a )—, —C( ⁇ O)—, —C( ⁇ S)—, —O—, —Si(R a ) 2 —, —S( ⁇ O) x —, and —N(R a )—;
  • x 0, 1, or 2;
  • n 1, 2, 3, or 4;
  • each R a and R b is, independently, H, a protecting group, hydroxyl, C 1 -C 12 alkyl, substituted C 1 -C 12 alkyl, C 2 -C 12 alkenyl, substituted C 2 -C 12 alkenyl, C 2 -C 12 alkynyl, substituted C 2 -C 12 alkynyl, C 5 -C 20 aryl, substituted C 5 -C 20 aryl, heterocycle radical, substituted heterocycle radical, heteroaryl, substituted heteroaryl, C 5 -C 7 alicyclic radical, substituted C 5 -C 7 alicyclic radical, halogen, OJ 1 , NJ 1 J 2 , SJ 1 , N 3 , COOJ 1 , acyl (C( ⁇ O)—H), substituted acyl, CN, sulfonyl (S( ⁇ O) 2 -J 1 ), or sulfoxyl (S( ⁇ O)-J 1 ); and each
  • bicyclic sugar moieties and nucleosides incorporating such bicyclic sugar moieties are further defined by isomeric configuration.
  • an LNA nucleoside (described herein) may be in the ⁇ -L configuration or in the ⁇ -D configuration.
  • bicyclic nucleosides include both isomeric configurations.
  • positions of specific bicyclic nucleosides e.g., LNA or cEt
  • they are in the ⁇ -D configuration, unless otherwise specified.
  • modified sugar moieties comprise one or more non-bridging sugar substituent and one or more bridging sugar substituent (e.g., 5′-substituted and 4′-2′ bridged sugars).
  • modified sugar moieties are sugar surrogates.
  • the oxygen atom of the sugar moiety is replaced, e.g., with a sulfur, carbon or nitrogen atom.
  • such modified sugar moieties also comprise bridging and/or non-bridging substituents as described herein.
  • certain sugar surrogates comprise a 4′-sulfur atom and a substitution at the 2′-position (see, e.g., Bhat et al., U.S. Pat. No. 7,875,733 and Bhat et al., U.S. Pat. No. 7,939,677) and/or the 5′ position.
  • sugar surrogates comprise rings having other than 5 atoms.
  • a sugar surrogate comprises a six-membered tetrahydropyran (“THP”).
  • TTP tetrahydropyrans
  • Such tetrahydropyrans may be further modified or substituted.
  • Nucleosides comprising such modified tetrahydropyrans include but are not limited to hexitol nucleic acid (“HNA”), anitol nucleic acid (“ANA”), manitol nucleic acid (“MNA”) (see e.g., Leumann, C J. Bioorg . & Med. Chem. 2002, 10, 841-854), fluoro HNA:
  • F-HNA see e.g., Swayze et al., U.S. Pat. No. 8,088,904; Swayze et al., U.S. Pat. No. 8,440,803; and Swayze et al., U.S. Pat. No. 9,005,906, F-HNA can also be referred to as a F-THP or 3′-fluoro tetrahydropyran), and nucleosides comprising additional modified THP compounds having the formula:
  • Bx is a nucleobase moiety
  • modified THP nucleosides are provided wherein q 1 , q 2 , q 3 , q 4 , q 5 , q 6 and q 7 are each H. In certain embodiments, at least one of q 1 , q 2 , q 3 , q 4 , q 5 , q 6 and q 7 is other than H. In certain embodiments, at least one of q 1 , q 2 , q 3 , q 4 , q 5 , q 6 and q 7 is methyl. In certain embodiments, modified THP nucleosides are provided wherein one of R 1 and R 2 is F. In certain embodiments, R 1 is F and R 2 is H, in certain embodiments, R 1 is methoxy and R 2 is H, and in certain embodiments, R 1 is methoxyethoxy and R 2 is H.
  • sugar surrogates comprise rings having more than 5 atoms and more than one heteroatom.
  • nucleosides comprising morpholino sugar moieties and their use in oligonucleotides have been reported (see, e.g., Braasch et al., Biochemistry, 2002, 41, 4503-4510 and Summerton et al., U.S. Pat. No. 5,698,685; Summerton et al., U.S. Pat. No. 5,166,315; Summerton et al., U.S. Pat. No. 5,185,444; and Summerton et al., U.S. 5,034,506).
  • morpholino means a sugar surrogate having the following structure:
  • morpholinos may be modified, for example by adding or altering various substituent groups from the above morpholino structure.
  • sugar surrogates are referred to herein as “modified morpholinos.”
  • sugar surrogates comprise acyclic moieties.
  • nucleosides and oligonucleotides comprising such acyclic sugar surrogates include but are not limited to: peptide nucleic acid (“PNA”), acyclic butyl nucleic acid (see, e.g., Kumar et al., Org. Biomol. Chem., 2013, 11, 5853-5865), and nucleosides and oligonucleotides described in Manoharan et al., US2013/130378.
  • Nucleobase (or base) modifications or substitutions are structurally distinguishable from, yet functionally interchangeable with, naturally occurring or synthetic unmodified nucleobases. Both natural and modified nucleobases are capable of participating in hydrogen bonding. Such nucleobase modifications can impart nuclease stability, binding affinity or some other beneficial biological property to antisense compounds.
  • compounds described herein comprise modified oligonucleotides.
  • modified oligonucleotides comprise one or more nucleoside comprising an unmodified nucleobase.
  • modified oligonucleotides comprise one or more nucleoside comprising a modified nucleobase.
  • modified oligonucleotides comprise one or more nucleoside that does not comprise a nucleobase, referred to as an abasic nucleoside.
  • modified nucleobases are selected from: 5-substituted pyrimidines, 6-azapyrimidines, alkyl or alkynyl substituted pyrimidines, alkyl substituted purines, and N-2, N-6 and 0-6 substituted purines.
  • modified nucleobases are selected from: 2-aminopropyladenine, 5-hydroxymethyl cytosine, 5-methylcytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-N-methylguanine, 6-N-methyladenine, 2-propyladenine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-propynyl (C ⁇ C—CH 3 ) uracil, 5-propynylcytosine, 6-azouracil, 6-azocytosine, 6-azothymine, 5-ribosyluracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl, 8-aza and other 8-substituted purines, 5-halo, particularly 5-bromo, 5-trifluoromethyl, 5-halouracil, and 5-halocytosine, 7-methylguanine
  • nucleobases include tricyclic pyrimidines, such as 1,3-diazaphenoxazine-2-one, 1,3-diazaphenothiazine-2-one and 9-(2-aminoethoxy)-1,3-diazaphenoxazine-2-one (G-clamp).
  • Modified nucleobases may also include those in which the purine or pyrimidine base is replaced with other heterocycles, for example 7-deaza-adenine, 7-deazaguanosine, 2-aminopyridine and 2-pyridone.
  • Further nucleobases include those disclosed in Merigan et al., U.S. Pat. No.
  • compounds targeted to a IRF4 nucleic acid comprise one or more modified nucleobases.
  • the modified nucleobase is 5-methylcytosine.
  • each cytosine is a 5-methylcytosine.
  • RNA and DNA are a 3′ to 5′ phosphodiester linkage
  • compounds described herein having one or more modified, i.e. non-naturally occurring, internucleoside linkages are often selected over compounds having naturally occurring internucleoside linkages because of desirable properties such as, for example, enhanced cellular uptake, enhanced affinity for target nucleic acids, and increased stability in the presence of nucleases.
  • internucleoside linkages having a chiral center include but are not limited to alkylphosphonates and phosphorothioates.
  • Modified oligonucleotides comprising internucleoside linkages having a chiral center can be prepared as populations of modified oligonucleotides comprising stereorandom internucleoside linkages, or as populations of modified oligonucleotides comprising phosphorothioate linkages in particular stereochemical configurations.
  • populations of modified oligonucleotides comprise phosphorothioate internucleoside linkages wherein all of the phosphorothioate internucleoside linkages are stereorandom.
  • modified oligonucleotides can be generated using synthetic methods that result in random selection of the stereochemical configuration of each phosphorothioate linkage. Nonetheless, as is well understood by those of skill in the art, each individual phosphorothioate of each individual oligonucleotide molecule has a defined stereoconfiguration.
  • populations of modified oligonucleotides are enriched for modified oligonucleotides comprising one or more particular phosphorothioate internucleoside linkages in a particular, independently selected stereochemical configuration.
  • the particular configuration of the particular phosphorothioate linkage is present in at least 65% of the molecules in the population.
  • the particular configuration of the particular phosphorothioate linkage is present in at least 70% of the molecules in the population. In certain embodiments, the particular configuration of the particular phosphorothioate linkage is present in at least 80% of the molecules in the population. In certain embodiments, the particular configuration of the particular phosphorothioate linkage is present in at least 90% of the molecules in the population. In certain embodiments, the particular configuration of the particular phosphorothioate linkage is present in at least 99% of the molecules in the population.
  • modified oligonucleotides can be generated using synthetic methods known in the art, e.g., methods described in Oka et al., JACS 125, 8307 (2003), Wan et al. Nuc. Acid. Res. 42, 13456 (2014), and WO 2017/015555.
  • a population of modified oligonucleotides is enriched for modified oligonucleotides having at least one indicated phosphorothioate in the (Sp) configuration.
  • a population of modified oligonucleotides is enriched for modified oligonucleotides having at least one phosphorothioate in the (Rp) configuration.
  • modified oligonucleotides comprising (Rp) and/or (Sp) phosphorothioates comprise one or more of the following formulas, respectively, wherein “B” indicates a nucleobase:
  • chiral internucleoside linkages of modified oligonucleotides described herein can be stereorandom or in a particular stereochemical configuration.
  • compounds targeted to an IRF4 nucleic acid comprise one or more modified internucleoside linkages.
  • the modified internucleoside linkages are phosphorothioate linkages.
  • each internucleoside linkage of an antisense compound is a phosphorothioate internucleoside linkage.
  • compounds described herein comprise oligonucleotides.
  • Oligonucleotides having modified internucleoside linkages include internucleoside linkages that retain a phosphorus atom as well as internucleoside linkages that do not have a phosphorus atom.
  • Representative phosphorus containing internucleoside linkages include, but are not limited to, phosphodiesters, phosphotriesters, methylphosphonates, phosphoramidate, and phosphorothioates. Methods of preparation of phosphorous-containing and non-phosphorous-containing linkages are well known.
  • nucleosides of modified oligonucleotides may be linked together using any internucleoside linkage.
  • the two main classes of internucleoside linking groups are defined by the presence or absence of a phosphorus atom.
  • Representative phosphorus-containing internucleoside linkages include but are not limited to phosphates, which contain a phosphodiester bond (“P ⁇ O”) (also referred to as unmodified or naturally occurring linkages), phosphotriesters, methylphosphonates, phosphoramidates, and phosphorothioates (“P ⁇ S”), and phosphorodithioates (“HS-P ⁇ S”).
  • Non-phosphorus containing internucleoside linking groups include but are not limited to methylenemethylimino (—CH2-N(CH3)-O—CH2-), thiodiester, thionocarbamate (—O—C( ⁇ O)(NH)—S—); siloxane (—O—SiH2-O—); and N,N′-dimethylhydrazine (—CH2-N(CH3)-N(CH3)-).
  • Modified internucleoside linkages compared to naturally occurring phosphate linkages, can be used to alter, typically increase, nuclease resistance of the oligonucleotide.
  • internucleoside linkages having a chiral atom can be prepared as a racemic mixture, or as separate enantiomers.
  • Representative chiral internucleoside linkages include but are not limited to alkylphosphonates and phosphorothioates. Methods of preparation of phosphorous-containing and non-phosphorous-containing internucleoside linkages are well known to those skilled in the art.
  • Neutral internucleoside linkages include, without limitation, phosphotriesters, methylphosphonates, MMI (3′-CH 2 —N(CH3)-O-5′), amide-3 (3′-CH2-C( ⁇ O)—N(H)-5′), amide-4 (3′-CH2-N(H)—C( ⁇ O)-5′), formacetal (3′-O-CH2-O-5′), methoxypropyl, and thioformacetal (3′-S—CH2-O-5′).
  • Further neutral internucleoside linkages include nonionic linkages comprising siloxane (dialkylsiloxane), carboxylate ester, carboxamide, sulfide, sulfonate ester and amides (See for example: Carbohydrate Modifications in Antisense Research; Y. S. Sanghvi and P. D. Cook, Eds., ACS Symposium Series 580; Chapters 3 and 4, 40-65). Further neutral internucleoside linkages include nonionic linkages comprising mixed N, O, S and CH2 component parts.
  • oligonucleotides comprise modified internucleoside linkages arranged along the oligonucleotide or region thereof in a defined pattern or modified internucleoside linkage motif.
  • internucleoside linkages are arranged in a gapped motif.
  • the internucleoside linkages in each of two wing regions are different from the internucleoside linkages in the gap region.
  • the internucleoside linkages in the wings are phosphodiester and the internucleoside linkages in the gap are phosphorothioate.
  • the nucleoside motif is independently selected, so such oligonucleotides having a gapped internucleoside linkage motif may or may not have a gapped nucleoside motif and if it does have a gapped nucleoside motif, the wing and gap lengths may or may not be the same.
  • oligonucleotides comprise a region having an alternating internucleoside linkage motif. In certain embodiments, oligonucleotides comprise a region of uniformly modified internucleoside linkages. In certain such embodiments, the oligonucleotide comprises a region that is uniformly linked by phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide is uniformly linked by phosphorothioate. In certain embodiments, each internucleoside linkage of the oligonucleotide is selected from phosphodiester and phosphorothioate. In certain embodiments, each internucleoside linkage of the oligonucleotide is selected from phosphodiester and phosphorothioate and at least one internucleoside linkage is phosphorothioate.
  • the oligonucleotide comprises at least 6 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least 8 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least 10 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least one block of at least 6 consecutive phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least one block of at least 8 consecutive phosphorothioate internucleoside linkages.
  • the oligonucleotide comprises at least one block of at least 10 consecutive phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least block of at least one 12 consecutive phosphorothioate internucleoside linkages. In certain such embodiments, at least one such block is located at the 3′ end of the oligonucleotide. In certain such embodiments, at least one such block is located within 3 nucleosides of the 3′ end of the oligonucleotide.
  • oligonucleotides comprise one or more methylphosphonate linkages.
  • oligonucleotides having a gapmer nucleoside motif comprise a linkage motif comprising all phosphorothioate linkages except for one or two methylphosphonate linkages.
  • one methylphosphonate linkage is in the central gap of an oligonucleotide having a gapmer nucleoside motif.
  • the number of phosphorothioate internucleoside linkages may be decreased and the number of phosphodiester internucleoside linkages may be increased while still maintaining nuclease resistance. In certain embodiments it is desirable to decrease the number of phosphorothioate internucleoside linkages while retaining nuclease resistance. In certain embodiments it is desirable to increase the number of phosphodiester internucleoside linkages while retaining nuclease resistance.
  • compounds described herein comprise oligonucleotides.
  • Oligonucleotides can have a motif, e.g. a pattern of unmodified and/or modified sugar moieties, nucleobases, and/or internucleoside linkages.
  • modified oligonucleotides comprise one or more modified nucleoside comprising a modified sugar.
  • modified oligonucleotides comprise one or more modified nucleosides comprising a modified nucleobase.
  • modified oligonucleotides comprise one or more modified internucleoside linkage.
  • the modified, unmodified, and differently modified sugar moieties, nucleobases, and/or internucleoside linkages of a modified oligonucleotide define a pattern or motif.
  • the patterns of sugar moieties, nucleobases, and internucleoside linkages are each independent of one another.
  • a modified oligonucleotide may be described by its sugar motif, nucleobase motif and/or internucleoside linkage motif (as used herein, nucleobase motif describes the modifications to the nucleobases independent of the sequence of nucleobases).
  • compounds described herein comprise oligonucleotides.
  • oligonucleotides comprise one or more type of modified sugar and/or unmodified sugar moiety arranged along the oligonucleotide or region thereof in a defined pattern or sugar motif.
  • sugar motifs include but are not limited to any of the sugar modifications discussed herein.
  • modified oligonucleotides comprise or consist of a region having a gapmer motif, which comprises two external regions or “wings” and a central or internal region or “gap.”
  • the three regions of a gapmer motif (the 5′-wing, the gap, and the 3′-wing) form a contiguous sequence of nucleosides wherein at least some of the sugar moieties of the nucleosides of each of the wings differ from at least some of the sugar moieties of the nucleosides of the gap.
  • the sugar moieties of the nucleosides of each wing that are closest to the gap differ from the sugar moiety of the neighboring gap nucleosides, thus defining the boundary between the wings and the gap (i.e., the wing/gap junction).
  • the sugar moieties within the gap are the same as one another.
  • the gap includes one or more nucleoside having a sugar moiety that differs from the sugar moiety of one or more other nucleosides of the gap.
  • the sugar motifs of the two wings are the same as one another (symmetric gapmer).
  • the sugar motif of the 5′-wing differs from the sugar motif of the 3′-wing (asymmetric gapmer).
  • the wings of a gapmer comprise 1-5 nucleosides. In certain embodiments, the wings of a gapmer comprise 2-5 nucleosides. In certain embodiments, the wings of a gapmer comprise 3-5 nucleosides. In certain embodiments, the nucleosides of a gapmer are all modified nucleosides.
  • the gap of a gapmer comprises 7-12 nucleosides. In certain embodiments, the gap of a gapmer comprises 7-10 nucleosides. In certain embodiments, the gap of a gapmer comprises 8-10 nucleosides. In certain embodiments, the gap of a gapmer comprises 10 nucleosides. In certain embodiment, each nucleoside of the gap of a gapmer is an unmodified 2′-deoxy nucleoside.
  • the gapmer is a deoxy gapmer.
  • the nucleosides on the gap side of each wing/gap junction are unmodified 2′-deoxy nucleosides and the nucleosides on the wing sides of each wing/gap junction are modified nucleosides.
  • each nucleoside of the gap is an unmodified 2′-deoxy nucleoside.
  • each nucleoside of each wing is a modified nucleoside.
  • a modified oligonucleotide has a fully modified sugar motif wherein each nucleoside of the modified oligonucleotide comprises a modified sugar moiety.
  • modified oligonucleotides comprise or consist of a region having a fully modified sugar motif wherein each nucleoside of the region comprises a modified sugar moiety.
  • modified oligonucleotides comprise or consist of a region having a fully modified sugar motif, wherein each nucleoside within the fully modified region comprises the same modified sugar moiety, referred to herein as a uniformly modified sugar motif.
  • a fully modified oligonucleotide is a uniformly modified oligonucleotide.
  • each nucleoside of a uniformly modified comprises the same 2′-modification.
  • a modified oligonucleotide can comprise a sugar motif described in Swayze et al., US2010/0197762; Freier et al., US2014/0107330; Freier et al., US2015/0184153; and Seth et al., US2015/0267195, each of which is incorporated by reference in its entirety herein.
  • modified oligomeric compounds useful for inhibiting target nucleic acid expression which can be useful for treating, preventing, ameliorating, or slowing progression of a disease associated with such a target nucleic acid.
  • the modified oligomeric compounds comprise antisense oligonucleotides that are gapmers having certain sugar motifs.
  • the gapmer sugar motifs provided herein can be combined with any nucleobase sequence and any internucleoside linkage motif to form potent antisense oligonucleotides.
  • a method comprises contacting a cell or administering to a subject a compound comprising a modified oligonucleotide 16 linked nucleosides in length having the motif: ekk-d9-kkee, wherein ‘d’ represents a 2′-deoxyribose sugar, ‘k’ represents a cEt nucleoside, and ‘e’ represents a 2′-MOE nucleoside.
  • the cell is a cancer cell.
  • the subject has cancer.
  • administering the compound to the subject treats the subject's cancer.
  • a method comprises contacting a cell or administering to a subject a compound comprising a modified oligonucleotide 16 linked nucleosides in length having the motif: k-d9-kekeke, wherein represents a 2′-deoxyribose sugar, ‘k’ represents a cEt nucleoside, and ‘e’ represents a 2′-MOE nucleoside.
  • the cell is a cancer cell.
  • the subject has cancer.
  • administering the compound to the subject treats the subject's cancer.
  • a method comprises contacting a cell or administering to a subject a compound comprising a modified oligonucleotide 16 linked nucleosides in length having the motif: kkk-d8-kekek, wherein ‘d’ represents a 2′-deoxyribose sugar, ‘k’ represents a cEt nucleoside, and ‘e’ represents a 2′-MOE nucleoside.
  • the cell is a cancer cell.
  • the subject has cancer.
  • administering the compound to the subject treats the subject's cancer.
  • a method comprises contacting a cell or administering to a subject a compound comprising a modified oligonucleotide 16 linked nucleosides in length having the motif: kkk-d9-keke, wherein ‘d’ represents a 2′-deoxyribose sugar, ‘k’ represents a cEt nucleoside, and ‘e’ represents a 2′-MOE nucleoside.
  • the cell is a cancer cell.
  • the subject has cancer.
  • administering the compound to the subject treats the subject's cancer.
  • a method comprises contacting a cell or administering to a subject a compound comprising a modified oligonucleotide 16 linked nucleosides in length having the motif: kk-d9-kdkdk, wherein ‘d’ represents a 2′-deoxyribose sugar, ‘k’ represents a cEt nucleoside, and ‘e’ represents a 2′-MOE nucleoside.
  • the cell is a cancer cell.
  • the subject has cancer.
  • administering the compound to the subject treats the subject's cancer.
  • a compound comprises a modified oligonucleotide 16 linked nucleosides in length having the motif: kk-d9-eeekk, wherein ‘d’ represents a 2′-deoxyribose sugar, ‘k’ represents a cEt nucleoside, and ‘e’ represents a 2′-MOE nucleoside.
  • a method comprises contacting a cell or administering to a subject a compound comprising a modified oligonucleotide 16 linked nucleosides in length having the motif: kk-d9-eeekk, wherein ‘d’ represents a 2′-deoxyribose sugar, ‘k’ represents a cEt nucleoside, and ‘e’ represents a 2′-MOE nucleoside.
  • the cell is a cancer cell.
  • the subject has cancer.
  • administering the compound to the subject treats the subject's cancer.
  • a method comprises contacting a cell or administering to a subject a compound comprising a modified oligonucleotide 16 linked nucleosides in length having the motif: kk-d9-kdkdk, wherein ‘d’ represents a 2′-deoxyribose sugar, ‘k’ represents a cEt nucleoside, and ‘e’ represents a 2′-MOE nucleoside.
  • the cell is a cancer cell.
  • the subject has cancer.
  • administering the compound to the subject treats the subject's cancer.
  • compounds described herein comprise oligonucleotides.
  • oligonucleotides comprise modified and/or unmodified nucleobases arranged along the oligonucleotide or region thereof in a defined pattern or motif.
  • each nucleobase is modified.
  • none of the nucleobases are modified.
  • each purine or each pyrimidine is modified.
  • each adenine is modified.
  • each guanine is modified.
  • each thymine is modified.
  • each uracil is modified.
  • each cytosine is modified.
  • some or all of the cytosine nucleobases in a modified oligonucleotide are 5-methylcytosines.
  • modified oligonucleotides comprise a block of modified nucleobases.
  • the block is at the 3′-end of the oligonucleotide. In certain embodiments the block is within 3 nucleosides of the 3′-end of the oligonucleotide. In certain embodiments, the block is at the 5′-end of the oligonucleotide. In certain embodiments the block is within 3 nucleosides of the 5′-end of the oligonucleotide.
  • oligonucleotides having a gapmer motif comprise a nucleoside comprising a modified nucleobase.
  • one nucleoside comprising a modified nucleobase is in the central gap of an oligonucleotide having a gapmer motif.
  • the sugar moiety of said nucleoside is a 2′-deoxyribosyl moiety.
  • the modified nucleobase is selected from: a 2-thiopyrimidine and a 5-propynepyrimidine.
  • compounds described herein comprise oligonucleotides.
  • oligonucleotides comprise modified and/or unmodified internucleoside linkages arranged along the oligonucleotide or region thereof in a defined pattern or motif.
  • essentially each internucleoside linking group is a phosphate internucleoside linkage (P ⁇ O).
  • each internucleoside linking group of a modified oligonucleotide is a phosphorothioate (P ⁇ S).
  • each internucleoside linking group of a modified oligonucleotide is independently selected from a phosphorothioate and phosphate internucleoside linkage.
  • the sugar motif of a modified oligonucleotide is a gapmer and the internucleoside linkages within the gap are all modified.
  • some or all of the internucleoside linkages in the wings are unmodified phosphate linkages.
  • the terminal internucleoside linkages are modified.
  • compounds described herein comprise modified oligonucleotides.
  • the above modifications are incorporated into a modified oligonucleotide.
  • modified oligonucleotides are characterized by their modification, motifs, and overall lengths. In certain embodiments, such parameters are each independent of one another. Thus, unless otherwise indicated, each internucleoside linkage of an oligonucleotide having a gapmer sugar motif may be modified or unmodified and may or may not follow the gapmer modification pattern of the sugar modifications.
  • the internucleoside linkages within the wing regions of a sugar gapmer may be the same or different from one another and may be the same or different from the internucleoside linkages of the gap region of the sugar motif.
  • such gapmer oligonucleotides may comprise one or more modified nucleobase independent of the gapmer pattern of the sugar modifications.
  • an oligonucleotide is described by an overall length or range and by lengths or length ranges of two or more regions (e.g., a regions of nucleosides having specified sugar modifications), in such circumstances it may be possible to select numbers for each range that result in an oligonucleotide having an overall length falling outside the specified range. In such circumstances, both elements must be satisfied.
  • a modified oligonucleotide consists of 15-20 linked nucleosides and has a sugar motif consisting of three regions, A, B, and C, wherein region A consists of 2-6 linked nucleosides having a specified sugar motif, region B consists of 6-10 linked nucleosides having a specified sugar motif, and region C consists of 2-6 linked nucleosides having a specified sugar motif.
  • Such embodiments do not include modified oligonucleotides where A and C each consist of 6 linked nucleosides and B consists of 10 linked nucleosides (even though those numbers of nucleosides are permitted within the requirements for A, B, and C) because the overall length of such oligonucleotide is 22, which exceeds the upper limit of the overall length of the modified oligonucleotide (20).
  • a and C each consist of 6 linked nucleosides and B consists of 10 linked nucleosides (even though those numbers of nucleosides are permitted within the requirements for A, B, and C) because the overall length of such oligonucleotide is 22, which exceeds the upper limit of the overall length of the modified oligonucleotide (20).
  • a description of an oligonucleotide is silent with respect to one or more parameter, such parameter is not limited.
  • a modified oligonucleotide described only as having a gapmer sugar motif without further description may have any
  • the compounds described herein comprise or consist of an oligonucleotide (modified or unmodified) and optionally one or more conjugate groups and/or terminal groups.
  • Conjugate groups consist of one or more conjugate moiety and a conjugate linker which links the conjugate moiety to the oligonucleotide. Conjugate groups may be attached to either or both ends of an oligonucleotide and/or at any internal position. In certain embodiments, conjugate groups are attached to the 2′-position of a nucleoside of a modified oligonucleotide. In certain embodiments, conjugate groups that are attached to either or both ends of an oligonucleotide are terminal groups.
  • conjugate groups or terminal groups are attached at the 3′ and/or 5′-end of oligonucleotides. In certain such embodiments, conjugate groups (or terminal groups) are attached at the 3′-end of oligonucleotides. In certain embodiments, conjugate groups are attached near the 3′-end of oligonucleotides. In certain embodiments, conjugate groups (or terminal groups) are attached at the 5′-end of oligonucleotides. In certain embodiments, conjugate groups are attached near the 5′-end of oligonucleotides.
  • the oligonucleotide is modified.
  • the oligonucleotide of a compound has a nucleobase sequence that is complementary to a target nucleic acid.
  • oligonucleotides are complementary to a messenger RNA (mRNA).
  • mRNA messenger RNA
  • oligonucleotides are complementary to a sense transcript.
  • terminal groups include but are not limited to conjugate groups, capping groups, phosphate moieties, protecting groups, modified or unmodified nucleosides, and two or more nucleosides that are independently modified or unmodified.
  • oligonucleotides are covalently attached to one or more conjugate groups.
  • conjugate groups modify one or more properties of the attached oligonucleotide, including but not limited to pharmacodynamics, pharmacokinetics, stability, binding, absorption, tissue distribution, cellular distribution, cellular uptake, charge and clearanceln certain embodiments, conjugate groups impart a new property on the attached oligonucleotide, e.g., fluorophores or reporter groups that enable detection of the oligonucleotide.
  • conjugate groups and conjugate moieties have been described previously, for example: cholesterol moiety (Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989, 86, 6553-6556), cholic acid (Manoharan et al., Bioorg. Med. Chem. Lett., 1994, 4, 1053-1060), a thioether, e.g., hexyl-S-tritylthiol (Manoharan et al., Ann. N.Y. Acad. Sci., 1992, 660, 306-309; Manoharan et al., Bioorg. Med. Chem.
  • Acids Res., 1990, 18, 3777-3783 a polyamine or a polyethylene glycol chain (Manoharan et al., Nucleosides & Nucleotides, 1995, 14, 969-973), or adamantane acetic, a palmityl moiety (Mishra et al., Biochim. Biophys. Acta, 1995, 1264, 229-237), an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety (Crooke et al., J. Pharmacol. Exp.
  • Conjugate moieties include, without limitation, intercalators, reporter molecules, polyamines, polyamides, peptides, carbohydrates (e.g., GalNAc), vitamin moieties, polyethylene glycols, thioethers, polyethers, cholesterols, thiocholesterols, cholic acid moieties, folate, lipids, phospholipids, biotin, phenazine, phenanthridine, anthraquinone, adamantane, acridine, fluoresceins, rhodamines, coumarins, fluorophores, and dyes.
  • intercalators include, without limitation, intercalators, reporter molecules, polyamines, polyamides, peptides, carbohydrates (e.g., GalNAc), vitamin moieties, polyethylene glycols, thioethers, polyethers, cholesterols, thiocholesterols, cholic acid moieties, folate, lipids, phospholipids, bio
  • a conjugate moiety comprises an active drug substance, for example, aspirin, warfarin, phenylbutazone, ibuprofen, suprofen, fen-bufen, ketoprofen, (S)-( ⁇ )-pranoprofen, carprofen, dansylsarcosine, 2,3,5-triiodobenzoic acid, fingolimod, flufenamic acid, folinic acid, a benzothiadiazide, chlorothiazide, a diazepine, indo-methicin, a barbiturate, a cephalosporin, a sulfa drug, an antidiabetic, an antibacterial or an antibiotic.
  • an active drug substance for example, aspirin, warfarin, phenylbutazone, ibuprofen, suprofen, fen-bufen, ketoprofen, (S)-( ⁇ )-pranoprofen, car
  • Conjugate moieties are attached to oligonucleotides through conjugate linkers.
  • a conjugate group is a single chemical bond (i.e. conjugate moiety is attached to an oligonucleotide via a conjugate linker through a single bond).
  • the conjugate linker comprises a chain structure, such as a hydrocarbyl chain, or an oligomer of repeating units such as ethylene glycol, nucleosides, or amino acid units.
  • a conjugate linker comprises one or more groups selected from alkyl, amino, oxo, amide, disulfide, polyethylene glycol, ether, thioether, and hydroxylamino. In certain such embodiments, the conjugate linker comprises groups selected from alkyl, amino, oxo, amide and ether groups. In certain embodiments, the conjugate linker comprises groups selected from alkyl and amide groups. In certain embodiments, the conjugate linker comprises groups selected from alkyl and ether groups. In certain embodiments, the conjugate linker comprises at least one phosphorus moiety. In certain embodiments, the conjugate linker comprises at least one phosphate group. In certain embodiments, the conjugate linker includes at least one neutral linking group.
  • conjugate linkers are bifunctional linking moieties, e.g., those known in the art to be useful for attaching conjugate groups to parent compounds, such as the oligonucleotides provided herein.
  • a bifunctional linking moiety comprises at least two functional groups. One of the functional groups is selected to bind to a particular site on a compound and the other is selected to bind to a conjugate group. Examples of functional groups used in a bifunctional linking moiety include but are not limited to electrophiles for reacting with nucleophilic groups and nucleophiles for reacting with electrophilic groups.
  • bifunctional linking moieties comprise one or more groups selected from amino, hydroxyl, carboxylic acid, thiol, alkyl, alkenyl, and alkynyl.
  • conjugate linkers include but are not limited to pyrrolidine, 8-amino-3,6-dioxaoctanoic acid (ADO), succinimidyl 4-(N-maleimidomethyl) cyclohexane-1-carboxylate (SMCC) and 6-aminohexanoic acid (AHEX or AHA).
  • ADO 8-amino-3,6-dioxaoctanoic acid
  • SMCC succinimidyl 4-(N-maleimidomethyl) cyclohexane-1-carboxylate
  • AHEX or AHA 6-aminohexanoic acid
  • conjugate linkers include but are not limited to substituted or unsubstituted C 1 -C 10 alkyl, substituted or unsubstituted C 2 -C 10 alkenyl or substituted or unsubstituted C 2 -C 10 alkynyl, wherein a nonlimiting list of preferred substituent groups includes hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro, thiol, thioalkoxy, halogen, alkyl, aryl, alkenyl and alkynyl.
  • conjugate linkers comprise 1-10 linker-nucleosides.
  • such linker-nucleosides are modified nucleosides.
  • such linker-nucleosides comprise a modified sugar moiety.
  • linker-nucleosides are unmodified.
  • linker-nucleosides comprise an optionally protected heterocyclic base selected from a purine, substituted purine, pyrimidine or substituted pyrimidine.
  • a cleavable moiety is a nucleoside selected from uracil, thymine, cytosine, 4-N-benzoylcytosine, 5-methylcytosine, 4-N-benzoyl-5-methylcytosine, adenine, 6-N-benzoyladenine, guanine and 2-N-isobutyrylguanine. It is typically desirable for linker-nucleosides to be cleaved from the compound after it reaches a target tissue. Accordingly, linker-nucleosides are typically linked to one another and to the remainder of the compound through cleavable bonds. In certain embodiments, such cleavable bonds are phosphodiester bonds.
  • linker-nucleosides are not considered to be part of the oligonucleotide. Accordingly, in embodiments in which a compound comprises an oligonucleotide consisting of a specified number or range of linked nucleosides and/or a specified percent complementarity to a reference nucleic acid and the compound also comprises a conjugate group comprising a conjugate linker comprising linker-nucleosides, those linker-nucleosides are not counted toward the length of the oligonucleotide and are not used in determining the percent complementarity of the oligonucleotide for the reference nucleic acid.
  • a compound may comprise (1) a modified oligonucleotide consisting of 8-30 nucleosides and (2) a conjugate group comprising 1-10 linker-nucleosides that are contiguous with the nucleosides of the modified oligonucleotide.
  • the total number of contiguous linked nucleosides in such a compound is more than 30.
  • an compound may comprise a modified oligonucleotide consisting of 8-30 nucleosides and no conjugate group.
  • the total number of contiguous linked nucleosides in such a compound is no more than 30.
  • conjugate linkers comprise no more than 10 linker-nucleosides.
  • conjugate linkers comprise no more than 5 linker-nucleosides. In certain embodiments, conjugate linkers comprise no more than 3 linker-nucleosides. In certain embodiments, conjugate linkers comprise no more than 2 linker-nucleosides. In certain embodiments, conjugate linkers comprise no more than 1 linker-nucleoside.
  • a conjugate group it is desirable for a conjugate group to be cleaved from the oligonucleotide. For example, in certain circumstances compounds comprising a particular conjugate moiety are better taken up by a particular cell type, but once the compound has been taken up, it is desirable that the conjugate group be cleaved to release the unconjugated or parent oligonucleotide.
  • certain conjugate may comprise one or more cleavable moieties, typically within the conjugate linker.
  • a cleavable moiety is a cleavable bond.
  • a cleavable moiety is a group of atoms comprising at least one cleavable bond.
  • a cleavable moiety comprises a group of atoms having one, two, three, four, or more than four cleavable bonds.
  • a cleavable moiety is selectively cleaved inside a cell or subcellular compartment, such as a lysosome.
  • a cleavable moiety is selectively cleaved by endogenous enzymes, such as nucleases.
  • a cleavable bond is selected from among: an amide, an ester, an ether, one or both esters of a phosphodiester, a phosphate ester, a carbamate, or a disulfide. In certain embodiments, a cleavable bond is one or both of the esters of a phosphodiester. In certain embodiments, a cleavable moiety comprises a phosphate or phosphodiester. In certain embodiments, the cleavable moiety is a phosphate linkage between an oligonucleotide and a conjugate moiety or conjugate group.
  • a cleavable moiety comprises or consists of one or more linker-nucleosides.
  • one or more linker-nucleosides are linked to one another and/or to the remainder of the compound through cleavable bonds.
  • such cleavable bonds are unmodified phosphodiester bonds.
  • a cleavable moiety is 2′-deoxy nucleoside that is attached to either the 3′ or 5′-terminal nucleoside of an oligonucleotide by a phosphate internucleoside linkage and covalently attached to the remainder of the conjugate linker or conjugate moiety by a phosphate or phosphorothioate linkage.
  • the cleavable moiety is 2′-deoxyadenosine.
  • compositions and methods for the formulation of pharmaceutical compositions are dependent upon a number of criteria, including, but not limited to, route of administration, extent of disease, or dose to be administered.
  • compositions comprising one or more compounds or a salt thereof.
  • the compounds are antisense compounds or oligomeric compounds.
  • the compounds comprise or consist of a modified oligonucleotide.
  • the pharmaceutical composition comprises a suitable pharmaceutically acceptable diluent or carrier.
  • a pharmaceutical composition comprises a sterile saline solution and one or more compound.
  • such pharmaceutical composition consists of a sterile saline solution and one or more compound.
  • the sterile saline is pharmaceutical grade saline.
  • a pharmaceutical composition comprises one or more compound and sterile water.
  • a pharmaceutical composition consists of one compound and sterile water.
  • the sterile water is pharmaceutical grade water.
  • a pharmaceutical composition comprises one or more compound and phosphate-buffered saline (PBS).
  • PBS phosphate-buffered saline
  • a pharmaceutical composition consists of one or more compound and sterile PBS.
  • the sterile PBS is pharmaceutical grade PBS.
  • a compound described herein targeted to IRF4 nucleic acid can be utilized in pharmaceutical compositions by combining the compound with a suitable pharmaceutically acceptable diluent or carrier.
  • a pharmaceutically acceptable diluent is water, such as sterile water suitable for injection.
  • employed in the methods described herein is a pharmaceutical composition comprising a compound targeted to IRF4 nucleic acid and a pharmaceutically acceptable diluent.
  • the pharmaceutically acceptable diluent is water.
  • the compound comprises or consists of a modified oligonucleotide provided herein.
  • compositions comprising compounds provided herein encompass any pharmaceutically acceptable salts, esters, or salts of such esters, or any other oligonucleotide which, upon administration to an animal, including a human, is capable of providing (directly or indirectly) the biologically active metabolite or residue thereof.
  • the compounds are antisense compounds or oligomeric compounds.
  • the compound comprises or consists of a modified oligonucleotide. Accordingly, for example, the disclosure is also drawn to pharmaceutically acceptable salts of compounds, prodrugs, pharmaceutically acceptable salts of such prodrugs, and other bioequivalents. Suitable pharmaceutically acceptable salts include, but are not limited to, sodium and potassium salts.
  • a prodrug can include the incorporation of additional nucleosides at one or both ends of a compound which are cleaved by endogenous nucleases within the body, to form the active compound.
  • the compounds or compositions further comprise a pharmaceutically acceptable carrier or diluent.
  • ION 690890, 935658, 935696, 935762, 935918, 935968, 882800, 1012795, 1014095, and 1014834 emerged as the top lead compounds.
  • ION 935918 exhibited the best combination of properties in terms of potency and tolerability out of over 3,000 oligonucleotides.
  • RNA nucleoside comprising a 2′-OH sugar moiety and a thymine base
  • RNA methylated uracil
  • nucleic acid sequences provided herein are intended to encompass nucleic acids containing any combination of natural or modified RNA and/or DNA, including, but not limited to such nucleic acids having modified nucleobases.
  • an oligonucleotide having the nucleobase sequence “ATCGATCG” encompasses any oligonucleotides having such nucleobase sequence, whether modified or unmodified, including, but not limited to, such compounds comprising RNA bases, such as those having sequence “AUCGAUCG” and those having some DNA bases and some RNA bases such as “AUCGATCG” and compounds having other modified nucleobases, such as “AT m CGAUCG,” wherein m C indicates a cytosine base comprising a methyl group at the 5-position.
  • Modified oligonucleotides complementary to a human IRF4 nucleic acid were designed and tested for their effect on IRF4 mRNA in vitro.
  • Human primer probe set RTS3114 forward sequence AAGCCTTGGCGTTCTCAGACT, designated herein as SEQ ID NO: 3386; reverse sequence TCAGCTCCTTCACGAGGATTTC, designated herein as SEQ ID NO: 3387; probe sequence CCGGCTGCACATCTGCCTGTACTACC, designated herein as SEQ ID: 3388
  • IRF4 mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN®. Results are presented in the table below as percent control of the amount of IRF4 mRNA, relative to untreated control (UTC) cells.
  • the modified oligonucleotides in Table 1 are 5-10-5 MOE gapmers.
  • the gapmers are 20 nucleobases in length, wherein the central gap segment comprises ten 2′-deoxynucleosides and is flanked by wing segments on both the 5′ end and on the 3′ end comprising five 2′-MOE nucleosides.
  • the sugar motif for the gapmers is (from 5′ to 3′): eeeeedddddddddddeeeee; wherein ‘d’ represents a 2′-deoxyribose sugar and ‘e’ represents a 2′-MOE modified sugar.
  • Each internucleoside linkage is a phosphorothioate internucleoside linkage and each cytosine residue is a 5-methylcytosine.
  • Start Site indicates the 5′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Sptop Site indicates the 3′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • modified oligonucleotide listed in Table 1 below is complementary to human IRF4 nucleic acid sequences SEQ ID NO: 1 or SEQ ID NO: 2, as indicated. ‘N/A’ indicates that the modified oligonucleotide is not complementary to that particular nucleic acid sequence with 100% complementarity. As shown below, modified oligonucleotides complementary to human IRF4 reduced the amount of human IRF4 mRNA.
  • Modified oligonucleotides complementary to a human IRF4 nucleic acid were designed and tested for their effect on IRF4 mRNA in vitro.
  • the modified oligonucleotides in Tables 2 and 3 are 3-10-3 cEt gapmers.
  • the gapmers are 16 nucleobases in length, wherein the central gap segment comprises ten 2′-deoxynucleosides and is flanked by wing segments on both the 5′ end and on the 3′ end comprising three cEt nucleosides.
  • the sugar motif for the gapmers is (from 5′ to 3′): kkkddddddddddddkkk; wherein ‘d’ represents a 2′-deoxyribose sugar and ‘k’ represents a cEt modified sugar.
  • Each internucleoside linkage is a phosphorothioate internucleoside linkage and each cytosine residue is a 5-methylcytosine.
  • Start Site indicates the 5′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Sptop Site indicates the 3′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • modified oligonucleotide listed in Tables 2 and 3 below is complementary to human IRF4 nucleic acid sequences SEQ ID NO: 1 or SEQ ID NO: 2, as indicated. ‘N/A’ indicates that the modified oligonucleotide is not complementary to that particular nucleic acid sequence with 100% complementarity. As shown below, modified oligonucleotides complementary to human IRF4 reduced the amount of human IRF4 mRNA.
  • Modified oligonucleotides complementary to a human IRF4 nucleic acid were designed and tested for their effect on IRF4 mRNA in vitro.
  • the modified oligonucleotides in Table 4 are 4-8-4 cEt gapmers.
  • the gapmers are 16 nucleobases in length, wherein the central gap segment comprises eight 2′-deoxynucleosides and is flanked by wing segments on both the 5′ end and on the 3′ end comprising four cEt nucleosides.
  • the sugar motif for the gapmers is (from 5′ to 3′): kkkkdddddddddkkkk; wherein ‘d’ represents a 2′-deoxyribose sugar and ‘k’ represents a cEt modified sugar.
  • Each internucleoside linkage is a phosphorothioate internucleoside linkage and each cytosine residue is a 5-methylcytosine.
  • Start Site indicates the 5′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Sptop Site indicates the 3′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • modified oligonucleotide listed in Table 4 below is complementary to human IRF4 nucleic acid sequences SEQ ID NO: 1 or SEQ ID NO: 2, as indicated. ‘N/A’ indicates that the modified oligonucleotide is not complementary to that particular nucleic acid sequence with 100% complementarity. As shown below, modified oligonucleotides complementary to human IRF4 reduced the amount of human IRF4 mRNA.
  • Modified oligonucleotides complementary to a human IRF4 nucleic acid were designed and tested for their effect on IRF4 mRNA in vitro.
  • the modified oligonucleotides in Tables 5 through 12 are 3-10-3 cEt gapmers.
  • the gapmers are 16 nucleobases in length, wherein the central gap segment comprises ten 2′-deoxynucleosides and is flanked by wing segments on both the 5′ end and on the 3′ end comprising three cEt nucleosides.
  • the sugar motif for the gapmers is (from 5′ to 3′): kkkddddddddddddkkk; wherein ‘d’ represents a 2′-deoxyribose sugar and ‘k’ represents a cEt modified sugar.
  • Each internucleoside linkage is a phosphorothioate internucleoside linkage and each cytosine residue is a 5-methylcytosine.
  • Start Site indicates the 5′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Sptop Site indicates the 3′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • modified oligonucleotide listed in Tables 5 through 12 below is complementary to human IRF4 nucleic acid sequences SEQ ID NO: 1 or SEQ ID NO: 2, as indicated. ‘N/A’ indicates that the modified oligonucleotide is not complementary to that particular nucleic acid sequence with 100% complementarity. As shown below, modified oligonucleotides complementary to human IRF4 reduced the amount of human IRF4 mRNA.
  • Modified oligonucleotides complementary to a human IRF4 nucleic acid were designed and tested for their effect on IRF4 mRNA in vitro.
  • the modified oligonucleotides in Tables 13 through 24 are 3-10-3 cEt gapmers.
  • the gapmers are 16 nucleobases in length, wherein the central gap segment comprises ten 2′-deoxynucleosides and is flanked by wing segments on both the 5′ end and on the 3′ end comprising three cEt nucleosides.
  • the sugar motif for the gapmers is (from 5′ to 3′): kkkddddddddddddkkk; wherein represents a 2′-deoxyribose sugar and ‘k’ represents a cEt modified sugar.
  • Each internucleoside linkage is a phosphorothioate internucleoside linkage and each cytosine residue is a 5-methylcytosine.
  • Start Site indicates the 5′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Sptop Site indicates the 3′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • modified oligonucleotide listed in Tables 13 through 24 below is complementary to human IRF4 nucleic acid sequences SEQ ID NO: 1 or SEQ ID NO: 2, as indicated. ‘N/A’ indicates that the modified oligonucleotide is not complementary to that particular nucleic acid sequence with 100% complementarity. As shown below, modified oligonucleotides complementary to human IRF4 reduced the amount of human IRF4 mRNA.
  • Modified oligonucleotides complementary to a human IRF4 nucleic acid were designed and tested for their effect on IRF4 mRNA in vitro.
  • the modified oligonucleotides in Tables 25 through 36 are 3-10-3 cEt gapmers.
  • the gapmers are 16 nucleobases in length, wherein the central gap segment comprises ten 2′-deoxynucleosides and is flanked by wing segments on both the 5′ end and on the 3′ end comprising three cEt nucleosides.
  • the sugar motif for the gapmers is (from 5′ to 3′): kkkddddddddddddkkk; wherein ‘d’ represents a 2′-deoxyribose sugar and ‘k’ represents a cEt modified sugar.
  • Each internucleoside linkage is a phosphorothioate internucleoside linkage and each cytosine residue is a 5-methylcytosine.
  • Start Site indicates the 5′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Sptop Site indicates the 3′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • modified oligonucleotide listed in Tables 25 through 36 below is complementary to human IRF4 nucleic acid sequences SEQ ID NO: 1 or SEQ ID NO: 2, as indicated. ‘N/A’ indicates that the modified oligonucleotide is not complementary to that particular nucleic acid sequence with 100% complementarity. As shown below, modified oligonucleotides complementary to human IRF4 reduced the amount of human IRF4 mRNA.
  • Modified oligonucleotides complementary to a human IRF4 nucleic acid were designed and tested for their effect on IRF4 mRNA in vitro.
  • MM.1R cells at a density of 5,000 cells per well were transfected by free uptake with 1,000 nM concentration of modified oligonucleotide or no modified oligonucleotide for untreated controls. After approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by quantitative real-time PCR.
  • Human primer probe set hIRF4_LTS34726 forward sequence GGCAAAGAAAGCTCATCACAG, designated herein as SEQ ID NO: 3389; reverse sequence GGATTGCTGATGTGTTCTGGTA designated herein as SEQ ID NO: 3390; probe sequence TAGCCCCTCAGGAAATGTCCACTG, designated herein as SEQ ID: 3391
  • IRF4 mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN®. Results are presented in the table below as percent control of the amount of IRF4 mRNA, relative to untreated control (UTC) cells.
  • the modified oligonucleotides in Table 37 are cEt and/or MOE containing gapmers.
  • the modified oligonucleotides have a central gap segment comprising 2′-deoxynucleosides which is flanked by wing segments on the 5′ direction and the 3′ direction. At least one nucleoside in the 5′ wing segment and/or one nucleoside in the 3′ wing segment has a MOE and/or cEt sugar modification.
  • the “Motif” column describes the sugar modifications of each oligonucleotide. “k” indicates a cEt sugar modification; “d” indicates deoxyribose; and “e” indicates a MOE modification.
  • Each internucleoside linkage is a phosphorothioate internucleoside linkage and each cytosine residue is a 5-methylcytosine.
  • Start Site indicates the 5′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Sptop Site indicates the 3′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • modified oligonucleotide listed in Table 37 below is complementary to human IRF4 nucleic acid sequences SEQ ID NO: 1 or SEQ ID NO: 2, as indicated. ‘N/A’ indicates that the modified oligonucleotide is not complementary to that particular nucleic acid sequence with 100% complementarity. As shown below, modified oligonucleotides complementary to human IRF4 reduced the amount of human IRF4 mRNA.
  • Modified oligonucleotides complementary to a human IRF4 nucleic acid were designed and tested for their effect on IRF4 mRNA in vitro.
  • MM.1R cells at a density of 5,000 cells per well were transfected by free uptake with 1,000 nM concentration of modified oligonucleotide or no modified oligonucleotide for untreated controls. After approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by quantitative real-time PCR. Human primer probe set hIRF4_LTS34726 (described hereinabove in Example 7) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN®. Results are presented in the table below as percent control of the amount of IRF4 mRNA, relative to untreated control (UTC) cells.
  • UTC untreated control
  • the modified oligonucleotides in Tables 38 through 42 are cEt and/or MOE containing gapmers.
  • the modified oligonucleotides have a central gap segment comprising 2′-deoxynucleosides which is flanked by wing segments on the 5′ direction and the 3′ direction. At least one nucleoside in the 5′ wing segment and/or one nucleoside in the 3′ wing segment has a MOE and/or cEt sugar modification.
  • the “Motif” column describes the sugar modifications of each oligonucleotide. “k” indicates a cEt sugar modification; “d” indicates deoxyribose; and “e” indicates a MOE modification.
  • Each internucleoside linkage is a phosphorothioate internucleoside linkage and each cytosine residue is a 5-methylcytosine.
  • Start Site indicates the 5′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Sptop Site indicates the 3′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • modified oligonucleotide listed in Tables 38 through 42 below is complementary to human IRF4 nucleic acid sequences SEQ ID NO: 1 or SEQ ID NO: 2, as indicated. ‘N/A’ indicates that the modified oligonucleotide is not complementary to that particular nucleic acid sequence with 100% complementarity. As shown below, modified oligonucleotides complementary to human IRF4 reduced the amount of human IRF4 mRNA.
  • Modified oligonucleotides complementary to a human IRF4 nucleic acid were designed and tested for their effect on IRF4 mRNA in vitro.
  • MM.1R cells at a density of 5,000 cells per well were transfected by free uptake with 1,000 nM concentration of modified oligonucleotide or no modified oligonucleotide for untreated controls. After approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by quantitative real-time PCR. Human primer probe set hIRF4_LTS34726 (described hereinabove in Example 7) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN®. Results are presented in the table below as percent control of the amount of IRF4 mRNA, relative to untreated control (UTC) cells.
  • UTC untreated control
  • the modified oligonucleotides in Tables 43 through 52 are 3-10-3 cEt gapmers.
  • the gapmers are 16 nucleobases in length, wherein the central gap segment comprises ten 2′-deoxynucleosides and is flanked by wing segments on both the 5′ end and on the 3′ end comprising three cEt nucleosides.
  • the sugar motif for the gapmers is (from 5′ to 3′): kkkddddddddddddkkk; wherein represents a 2′-deoxyribose sugar and ‘k’ represents a cEt modified sugar.
  • Each internucleoside linkage is a phosphorothioate internucleoside linkage and each cytosine residue is a 5-methylcytosine.
  • Start Site indicates the 5′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Sptop Site indicates the 3′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • modified oligonucleotide listed in Tables 43 through 52 below is complementary to human IRF4 nucleic acid sequences SEQ ID NO: 1 or SEQ ID NO: 2, as indicated. ‘N/A’ indicates that the modified oligonucleotide is not complementary to that particular nucleic acid sequence with 100% complementarity. As shown below, modified oligonucleotides complementary to human IRF4 reduced the amount of human IRF4 mRNA.
  • Modified oligonucleotides complementary to a human IRF4 nucleic acid were designed and tested for their effect on IRF4 mRNA in vitro.
  • MM.1R cells at a density of 5,000 cells per well were transfected by free uptake with 1,000 nM concentration of modified oligonucleotide or no modified oligonucleotide for untreated controls. After approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by quantitative real-time PCR. Human primer probe set hIRF4_LTS34726 (described hereinabove in Example 7) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN®. Results are presented in the tables below as percent control of the amount of IRF4 mRNA, relative to untreated control (UTC) cells.
  • UTC untreated control
  • the modified oligonucleotides in Tables 53 through 58 are cEt and/or MOE containing gapmers.
  • the modified oligonucleotides have a central gap segment comprising 2′-deoxynucleosides which is flanked by wing segments on the 5′ direction and the 3′ direction. At least one nucleoside in the 5′ wing segment and/or one nucleoside in the 3′ wing segment has a MOE and/or cEt sugar modification.
  • the “Motif” column describes the sugar modifications of each oligonucleotide. “k” indicates a cEt sugar modification; “d” indicates deoxyribose; and “c” indicates a MOE modification.
  • Each internucleoside linkage is a phosphorothioate internucleoside linkage and each cytosine residue is a 5-methylcytosine.
  • Start Site indicates the 5′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Sptop Site indicates the 3′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • modified oligonucleotide listed in Tables 53 through 58 below is complementary to human IRF4 nucleic acid sequences SEQ ID NO: 1 or SEQ ID NO: 2, as indicated. ‘N/A’ indicates that the modified oligonucleotide is not complementary to that particular nucleic acid sequence with 100% complementarity. As shown below, modified oligonucleotides complementary to human IRF4 reduced the amount of human IRF4 mRNA.
  • Modified oligonucleotides complementary to a human IRF4 nucleic acid were designed and tested for their effect on IRF4 mRNA in vitro.
  • MM.1R cells at a density of 5,000 cells per well were transfected by free uptake with 1,000 nM concentration of modified oligonucleotide or no modified oligonucleotide for untreated controls. After approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by quantitative real-time PCR.
  • Human primer probe set RTS4522 forward sequence CGGAAATCCCGTACCAATGT, designated herein as SEQ ID NO: 3392; reverse sequence TGGCAACCATTTTCACAAGCT designated herein as SEQ ID NO: 3393; probe sequence TTTGGACCCCGCGGCCAC, designated herein as SEQ ID: 3394
  • IRF4 mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN®. Results are presented in the tables below as percent control of the amount of IRF4 mRNA, relative to untreated control (UTC) cells.
  • the modified oligonucleotides in Tables 59 through 64 are cEt and/or MOE containing gapmers.
  • the modified oligonucleotides have a central gap segment comprising 2′-deoxynucleosides which is flanked by wing segments on the 5′ direction and the 3′ direction. At least one nucleoside in the 5′ wing segment and/or one nucleoside in the 3′ wing segment has a MOE and/or cEt sugar modification.
  • the “Motif” column describes the sugar modifications of each oligonucleotide. “k” indicates a cEt sugar modification; “d” indicates deoxyribose; and “e” indicates a MOE modification.
  • Each internucleoside linkage is a phosphorothioate internucleoside linkage and each cytosine residue is a 5-methylcytosine.
  • Start Site indicates the 5′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Sptop Site indicates the 3′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • modified oligonucleotide listed in Table 59 through 64 below is complementary to human IRF4 nucleic acid sequences SEQ ID NO: 1 or SEQ ID NO: 2, as indicated. ‘N/A’ indicates that the modified oligonucleotide is not complementary to that particular nucleic acid sequence with 100% complementarity. As shown below, modified oligonucleotides complementary to human IRF4 reduced the amount of human IRF4 mRNA.
  • Modified oligonucleotides selected from the examples above were tested at various doses in SK-MEL-28 cells.
  • Cells were plated at a density of 20,000 cells per well and transfected using electroporation with 185 nM, 555 nM, 1,666 nM, 5,000 nM, and 15,000 nM concentrations of modified oligonucleotide, as specified in the tables below.
  • RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR.
  • Human IRF4 primer probe set RTS3114 (described hereinabove in Example 1) was used to measure mRNA levels.
  • IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen. Results are presented as the percent level of IRF4 mRNA transcript, relative to that of untreated control (UTC) cells. As illustrated in the tables below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • Modified oligonucleotides selected from the examples above were tested at various doses in SK-MEL-28 cells.
  • Cells were plated at a density of 20,000 cells per well and transfected using electroporation with 500 nM, 1,000 nM, 2,000 nM, 4,000 nM, and 8,000 nM concentrations of modified oligonucleotide, as specified in the tables below.
  • RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR.
  • Human IRF4 primer probe set RTS3114 (described hereinabove in Example 1) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen.
  • Results are presented as the percent level of IRF4 mRNA transcript, relative to that of untreated control (UTC) cells. As illustrated in the tables below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • Modified oligonucleotides selected from the examples above were tested at various doses in SK-MEL-28 cells.
  • Cells were plated at a density of 20,000 cells per well and transfected using electroporation with 296 nM, 888 nM, 2,666 nM, and 8,000 nM concentrations of modified oligonucleotide, as specified in the tables below.
  • RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR.
  • Human IRF4 primer probe set RTS3114 (described hereinabove in Example 1) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen.
  • Results are presented as the percent level of IRF4 mRNA transcript, relative to that of untreated control (UTC) cells. As illustrated in the tables below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • Modified oligonucleotides selected from the examples above were tested at various doses in MM.1R cells.
  • Cells were plated at a density of 5,000 cells per well and transfected by free uptake with 74 nM, 222 nM, 666 nM, and 2,000 nM concentrations of modified oligonucleotide, as specified in the tables below.
  • RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR.
  • Human IRF4 primer probe set hIRF4_LTS34726 (described hereinabove in Example 7) was used to measure mRNA levels.
  • IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen. Results are presented as the percent level of IRF4 mRNA transcript, relative to that of untreated control (UTC) cells. As illustrated in the tables below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • Modified oligonucleotides selected from the examples above were tested at various doses in MM.1R cells.
  • Cells were plated at a density of 5,000 cells per well and transfected by free uptake with 74 nM, 222 nM, 666 nM, and 2,000 nM concentrations of modified oligonucleotide, as specified in the tables below.
  • RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR.
  • Human IRF4 primer probe set hIRF4_LTS34726 (described hereinabove in Example 7) was used to measure mRNA levels.
  • IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen. Results are presented as the percent level of IRF4 mRNA transcript, relative to that of untreated control (UTC) cells. As illustrated in the tables below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • Example 17 Design of 3-10-3 cEt Gapmers with Phosphorothioate Internucleoside Linkages
  • Modified oligonucleotides complementary to a human IRF4 nucleic acid were designed.
  • the modified oligonucleotides in Table 95 are 3-10-3 cEt gapmers.
  • the gapmers are 16 nucleobases in length, wherein the central gap segment comprises ten 2′-deoxynucleosides and is flanked by wing segments on both the 5′ end and on the 3′ end comprising three cEt nucleosides.
  • the sugar motif for the gapmers is (from 5′ to 3′): kkkddddddddddddkkk; wherein represents a 2′-deoxyribose sugar and ‘k’ represents a cEt modified sugar.
  • Each internucleoside linkage is a phosphorothioate internucleoside linkage and each cytosine residue is a 5-methylcytosine.
  • Start Site indicates the 5′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Sptop Site indicates the 3′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Each modified oligonucleotide listed in Table 95 below is complementary to human IRF4 nucleic acid sequences SEQ ID NO: 1 or SEQ ID NO: 2, as indicated. ‘N/A’ indicates that the modified oligonucleotide is not complementary to that particular nucleic acid sequence with 100% complementarity.
  • Modified oligonucleotides selected from the examples above were tested at various doses in MM.1R cells.
  • Cells were plated at a density of 5,000 cells per well and transfected by free uptake with 62.5 nM, 250 nM, 1,000 nM, and 4,000 nM concentrations of modified oligonucleotide, as specified in the tables below.
  • RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR.
  • Human IRF4 primer probe set hIRF4_LTS34726 (described hereinabove in Example 7) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen.
  • Results are presented as the percent level of IRF4 mRNA transcript, relative to that of untreated control (UTC) cells. As illustrated in the tables below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • Modified oligonucleotides selected from the examples above were tested at various doses in MM.1R cells.
  • Cells were plated at a density of 5,000 cells per well and transfected by free uptake with 62.5 nM, 250 nM, 1,000 nM, and 4,000 nM concentrations of modified oligonucleotide, as specified in the tables below.
  • RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR.
  • Human IRF4 primwr probe set RTS4523 (forward sequence AAGCCTTGGCGTTCTCAGACT, designated herein as SEQ ID NO: 3386; reverse sequence TCAGCTCCTTCACGAGGATTTC, designated herein as SEQ ID NO: 3387; probe sequence CCGGCTGCACATCTGCCTGTACTACC, designated herein as SEQ ID: 3388), was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen. Results are presented as the percent level of IRF4 mRNA transcript, relative to that of untreated control (UTC) cells. As illustrated in the table below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • Modified oligonucleotides selected from the examples above were tested at various doses in MM.1R cells.
  • Cells were plated at a density of 5,000 cells per well and transfected by free uptake with 62.5 nM, 250 nM, 1,000 nM, and 4,000 nM concentrations of modified oligonucleotide, as specified in the tables below.
  • RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR.
  • Human IRF4 primer probe set hIRF4_LTS34726 (described hereinabove in Example 7) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen.
  • Results are presented as the percent level of IRF4 mRNA transcript, relative to that of untreated control (UTC) cells. As illustrated in the tables below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • Modified oligonucleotides selected from the examples above were tested at various doses in MM.1R cells.
  • Cells were plated at a density of 5,000 cells per well and transfected by free uptake with 62.5 nM, 250 nM, 1,000 nM, and 4,000 nM concentrations of modified oligonucleotide, as specified in the tables below.
  • RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR.
  • Human IRF4 primer probe set RTS4523 (described hereinabove in Example 19) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen.
  • Results are presented as the percent level of IRF4 mRNA transcript, relative to that of untreated control (UTC) cells. As illustrated in the table below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • Modified oligonucleotides selected from the examples above were tested at various doses in MM.1R cells.
  • Cells were plated at a density of 5,000 cells per well and transfected by free uptake with 62.5 nM, 250 nM, 1,000 nM, and 4,000 nM concentrations of modified oligonucleotide, as specified in the tables below.
  • RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR.
  • Human IRF4 primer probe set RTS4522 (described hereinabove in Example 11) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen.
  • Results are presented as the percent level of IRF4 mRNA transcript, relative to that of untreated control (UTC) cells. As illustrated in the tables below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • Modified oligonucleotides selected from the examples above were tested at various doses in KMS11 cells for their effects on target knockdown and on cell line proliferation.
  • KMS11 cells were plated at a density of 10,000 cells per well and transfected by free uptake with 8 nM, 40 nM, 200 nM, and 1,000 nM concentrations of modified oligonucleotide, as specified in the tables below.
  • RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR.
  • Human IRF4 primer probe set RTS4522 (described hereinabove in Example 11) was used to measure mRNA levels.
  • IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen. Results are presented as the percent level of IRF4 mRNA transcript, relative to that of untreated control (UTC) cells.
  • UTC untreated control
  • KMS11 cells were plated at a density of 2,000 cells per well and transfected by free uptake with 8 nM, 40 nM, 200 nM, and 1,000 nM concentrations of modified oligonucleotide, as specified in the tables below. After seven days, CellTiterGlo-2.0 (Promega) was added and luminescence was measured on Glomax (Promega).
  • Modified oligonucleotides selected from the examples above were tested at various doses in H929 cells for their effects on target knockdown and on cell line proliferation.
  • H929 cells were plated at a density of 10,000 cells per well and transfected by free uptake with 8 nM, 40 nM, 200 nM, and 1,000 nM concentrations of modified oligonucleotide or 0.67 nM, 2 nM, 6.67 nM or 20 nM concentrations of modified oligonucleotide, as specified in the tables below.
  • RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR.
  • Human IRF4 primer probe set RTS4522 (described hereinabove in Example 11) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen.
  • Results are presented as the percent level of IRF4 mRNA transcript, relative to that of untreated control (UTC) cells. As illustrated in the tables below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • H929 cells were plated at a density of 2,000 cells per well and transfected by free uptake with 8 nM, 40 nM, 200 nM, and 1,000 nM concentrations of modified oligonucleotide, as specified in the tables below. After seven days, CellTiterGlo-2.0 (Promega) was added and luminescence was measured on Glomax (Promega).
  • Modified oligonucleotides selected from the examples above were tested at various doses in ABC-DLBCL lines U2932 and TMD8 for their effects on target knockdown and on cell line proliferation.
  • IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen. Results are presented as the percent level of IRF4 mRNA transcript, relative to untreated control (UTC) cells. As illustrated in the tables below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • Cells were plated at a density of 2,000 cells per well and transfected by free uptake with 50 nM, 200 nM, 1,000 nM, or 5,000 nM concentrations of modified oligonucleotide, as specified in the tables below. After seven days, CellTiterGlo-2.0 (Promega) was added and luminescence was measured on Glomax (Promega).
  • Modified oligonucleotides selected from the examples above were tested at various doses in ALCL cell lines for their effects on target knockdown and on cell line proliferation.
  • Human IRF4 primer probe set RTS4522 (described hereinabove in Example 11) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen.
  • Results are presented as the percent level of IRF4 mRNA transcript, relative to untreated control (UTC) cells.
  • IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • Cells were plated at a density of 2,000 cells per well and transfected by free uptake with 50 nM, 200 nM, 1,000 nM, or 5,000 nM concentrations of modified oligonucleotide, as specified in the tables below. After seven days, CellTiterGlo-2.0 (Promega) was added and luminescence was measured on Glomax (Promega).
  • Modified oligonucleotides selected from the examples above were tested at various doses in mantle cell lymphoma (MCL) lines MAVER1, JVM2, Granta519, Mino, and Z138 for their effects on target knockdown and on cell line proliferation.
  • MCL mantle cell lymphoma
  • IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen. Results are presented as the percent level of IRF4 mRNA transcript, relative to untreated control (UTC) cells. As illustrated in the tables below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • Cells were plated at a density of 2,000 cells per well and transfected by free uptake with 50 nM, 200 nM, 1,000 nM, or 5,000 nM concentrations of modified oligonucleotide, as specified in the tables below. After seven days, CellTiterGlo-2.0 (Promega) was added and luminescence was measured on Glomax (Promega).
  • Example 28 In Vivo Activity in MM1.R Xenograft Model
  • a xenograft MM1.R model was used to evaluate activity of modified oligonucleotides targeted to human IRF4.
  • Female NOD/SCID mice (JAX) at 4-6 weeks of age were given a subcuntaneous injection of 6 million MM1.R cells to form a xenograft tumor.
  • groups of 3 mice were administered 25, 50, or 100 mg/kg/dose modified oligonucleotide once a day for three days by subcutaneous injection.
  • One group of mice received subcutaneous injections of PBS once a day for three days.
  • the saline-injected group served as the control group to which oligonucleotide-treated groups were compared. Mice were sacrificed 48 hours after the final dose and tumors were collected for further analysis.
  • primer probe set 34726 described above in Example 7
  • primer probe set 35624 forward sequence TCCCGTGTTGCTTCAAACT, designated herein as SEQ ID NO: 3395
  • reverse sequence TACCTGCTGGCAGTTCTTTC designated herein as SEQ ID NO: 3396
  • probe sequence ACAGATGGGACTTAACAGGCAATGGG designated herein as SEQ ID: 3397
  • Results are presented as percent change of mRNA, relative to PBS control, normalized with human B-Actin levels from the human tumor cells and mouse stromal cells using human specific primer probe set 5002 (forward sequence CGGACTATGACTTAGTTGCGTTAC; designated herein as SEQ ID NO: 3398; reverse sequence GCCATGCCAATCTCATCTTGT, designated herein as SEQ ID NO: 3399; probe sequence CCTTTCTTGACAAAACCTAACTTGCGCAGA, designated herein as SEQ ID NO: 3400).
  • hIRF4 protein levels were measured in the xenograft tumors by a human-specific IRF4 antibody (abeam EP5699) on the WES system (ProteinSimple).
  • Ig ⁇ a clinically-relevant biomarker for MM
  • Example 29 Anti-Tumor Activity of Modified Oligonucleotides in a MM1.R Xenograft Model
  • a xenograft MM1.R model was used to evaluate activity of modified oligonucleotides targeted to human IRF4.
  • Female NOD-SCID mice at 5-6 weeks of age were given a subcuntaneous injection of 3 million MM1.R cells to form a xenograft tumor. 23 days later, groups of 8 mice were administered 50 mg/kg/dose modified oligonucleotide five times a week by subcutaneous injection for 3.5 weeks. One group of mice received subcutaneous injections of PBS five times a week. The saline-injected group served as the control group to which oligonucleotide-treated groups were compared. Tumor volume was estimated by caliper measurement. Mice were sacrificed 24 hours after the last dose and tissue was collected for RNA and protein analysis.
  • Body weights were measured throughout the study as a measure of tolerability.
  • ALT alanine transaminase
  • IRF4 mRNA in tumor samples was measured by RT-PCR using PPset RTS34726, described above.
  • IRF4 protein in tumor samples was determined by western blot as described in Example 28 above.
  • Example 30 Efficacy of modified oligonucleotides targeted to hIRF4 in a Systemically Disseminated MM1.R Model with Bone Marrow Involvement
  • a systemically disseminated MM1.R model was used to evaluate activity of modified oligonucleotides targeted to human IRF4.
  • Female nod-scid IL2R ⁇ null mice at 4-6 weeks of age were first administered 50 mg/kg cyclophosphamide on day 0, and on day 1 were administrated 10 million MM1.R cells via an intravenous injection.
  • plasma human Ig ⁇ was tested by ELISA and mice were randomized to groups based on these results.
  • groups of 4 mice were administered 50 mg/kg/day modified oligonucleotide once a day for three days, and sacrificed 48 hours after the last dose.
  • Levels of hIRF4 mRNA were measured in bone marrow.
  • the tumor burden was measured by measuring levels of hActin mRNA. Results are presented as percent change of mRNA, relative to PBS control treated mice.
  • Example 31 Efficacy of Modified Oligonucleotides Targeted to hIRF4 in a Systemically Disseminated MM1.R Model with Bone Marrow Involvement
  • a systemically disseminated MM1.R model was used to evaluate activity of modified oligonucleotides targeted to human IRF4.
  • Female NOD-SCID IL2R ⁇ null mice at 4-6 weeks of age were first administered 50 mg/kg cyclophosphamide on day 0, and on day 1 were administrated 10 million MM1.R cells via an intravenous injection.
  • serum human Ig ⁇ was tested by ELISA and mice were randomized to groups based on these results.
  • groups of ten mice were administered modified oligonucleotide with a loading dose of 50 mg/kg/day for 1 week, and then 3 doses a week at 50 mg/kg/day continuing until animal death, bodyweight drop of ⁇ 20% or paralysis.
  • One group often mice was administered PBS as a control, and another group was administered the control oligonucleotide 792169.
  • Example 32 Activity of Modified Oligonucleotides Targeting hIRF4 in a TMD8 Human ABC-DLBCL Tumor Model
  • a xenograft tumor model was used to evaluate activity of modified oligonucleotides targeted to human IRF4.
  • 4 million ABC-DLBCL TMD8 cells were implanted into the flanks of 5 week old female NOD/SCID mice. When tumors reached an average volume of 100 mm 3 , approximately two weeks post-implantation, groups of eight mice mice were administered 50 mg/kg/day modified oligonucleotide for two weeks. Mice were sacrificed after the last dose and tumors were collected for mRNA analysis.
  • Tumor volume was estimated with caliper measurement.
  • Levels of hIRF4 mRNA were measured in tumor tissue and normalized to control animals.
  • mice are frequently utilized for safety and efficacy testing.
  • the mice were treated with antisense oligonucleotides selected from studies described above and evaluated for changes in the levels of various plasma chemistry markers.
  • mice Groups of 4-6 week old male Balb/c mice were injected subcutaneously twice a week for four weeks with 50 mg/kg of modified oligonucleotides (100 mg/kg/week dose).
  • One group of male Balb/c mice was injected subcutaneously twice a week for 4 weeks with PBS. Mice were euthanized 48 hours after the last dose, and organs and plasma were harvested for further analysis.
  • modified oligonucleotides To evaluate the effect of modified oligonucleotides on liver and kidney function, plasma levels of transaminases, bilirubin, and BUN were measured using an automated clinical chemistry analyzer (Hitachi Olympus AU400e, Melville, N.Y.). The results are presented in the table below. Modified oligonucleotides that caused changes in the levels of any of the liver or kidney function markers outside the expected range for modified oligonucleotides were excluded in further studies.
  • Bil ID U/L (U/L) (mg/dL) (mg/dL) PBS 37 84 22.9 0.25 609296 n.d. n.d. n.d. n.d. 609343 n.d. n.d. n.d. n.d. 609354 n.d. n.d. n.d. n.d. 609357 n.d. n.d. n.d. n.d. n.d.
  • Bil ID U/L (U/L) (mg/dL) (mg/dL) PBS 35.8 53 21.1 0.25 666431 85.5 120 21.1 0.29 666440 8173 3432 26.2 3.84 666449 150 124 24.9 0.18 666471 n.d. n.d. n.d. n.d.
  • Bil ID U/L (U/L) (mg/dL) (mg/dL) PBS 32 89 24.1 0.29 609555 737 238 25.9 0.15 666772 n.d. n.d. n.d. n.d 666775 n.d. n.d. n.d. n.d 668818 n.d. n.d. n.d. n.d 668849 105 131 24.7 0.12 668850 547 394 27.8 0.11 668902 53 103 21.5 0.18 668934 n.d.
  • n.d. n.d. n.d 668936 2260 3211 24.8 0.13 668937 39 89 23.2 0.14 668947 n.d. n.d. n.d. n.d 668998 102 101 21.7 0.14 668999 625 404 28.9 0.21 669018 198 157 28.1 0.17 669022 33 60 19.9 0.19 669040 176 170 23.2 0.11 669066 589 300 23.8 0.27 669067 n.d. n.d. n.d 669068 95 137 20.0 0.16 669075 647 400 19.4 0.15
  • CD1® mice (Charles River, Mass.) are frequently utilized for safety and efficacy testing. The mice were treated with antisense oligonucleotides selected from studies described above and evaluated for changes in the levels of various plasma chemistry markers.
  • mice Groups of 4-6 week old male CD1 mice were injected subcutaneously twice a week for four weeks with 50 mg/kg of modified oligonucleotides (100 mg/kg/week dose).
  • One group of male CD1 mice was injected subcutaneously twice a week for 4 weeks with PBS. Mice were euthanized 48 hours after the last dose, and organs and plasma were harvested for further analysis.
  • modified oligonucleotides To evaluate the effect of modified oligonucleotides on liver and kidney function, plasma levels of transaminases, bilirubin, and BUN were measured using an automated clinical chemistry analyzer (Hitachi Olympus AU400e, Melville, N.Y.). The results are presented in the table below. Modified oligonucleotides that caused changes in the levels of any of the liver or kidney function markers outside the expected range for modified oligonucleotides were excluded in further studies.
  • n.d. n.d. n.d. 969938 1142 1009 18.1 0.76 970211 301 224 20.1 0.15 970249 1724 2104 20.0 6.21 970545 836 1049 24.8 0.34 970546 1248 1334 23.8 0.31 970547 878 665 18.4 0.53 970548 1607 3352 17.7 4.86 970552 n.d. n.d. n.d. n.d.
  • Sprague-Dawley rats are a multipurpose model used for safety and efficacy evaluations.
  • the rats were treated with modified antisense oligonucleotides from the studies described in the Examples above and evaluated for changes in the levels of various plasma chemistry markers.
  • ALT alanine transaminase
  • AST aspartate transaminase
  • BUN blood urea nitrogen
  • T. bilirubin Plasma levels of bilirubin were also measured using the same clinical chemistry analyzer and the results are also presented in the table below. Values represent the % change normalized to PBS-treated animals. Modified oligonucleotides that caused changes in the levels of any markers of liver function outside the expected range for antisense oligonucleotides were excluded in further studies.
  • Bil BUN Albumin ID (IU/L) (IU/L) (mg/dL) (mg/dL) (g/dL) PBS 47 67 0.14 16.4 3.92 690898 41 73 0.17 20.7 3.19 881413 42 61 0.18 18.1 3.66 881449 47 67 0.26 19.7 3.77 935658 47 55 0.16 17.4 3.80 935696 41 70 0.18 16.9 3.55 935898 72 81 0.19 18.0 4.23 935928 189 188 0.19 19.7 3.59 935968 39 85 0.21 17.2 3.61 936006 40 55 0.14 14.3 3.97
  • Bil BUN Albumin ID (IU/L) (IU/L) (mg/dL) (mg/dL) (g/dL) PBS 41 70 0.14 14.4 3.60 882408 38 68 0.15 17.0 2.80 1012795 25 70 0.09 22.3 2.47 1014095 37 101 0.12 20.3 2.41 1014393 41 70 0.09 20.3 2.28 1014394 32 74 0.08 21.1 2.53 1014834 34 68 0.10 14.2 3.04
  • Bil BUN Albumin ID (IU/L) (IU/L) (mg/dL) (mg/dL) (g/dL) PBS 55 51 0.15 17.1 3.04 935762 35 53 0.14 18.7 2.63 935918 31 55 0.15 19.7 2.60
  • HCT hematocrit
  • Liver, heart, spleen and kidney weights were measured at the end of the study, and are presented in the table below. Modified oligonucleotides that caused any changes in organ weights outside the expected range for antisense oligonucleotides were excluded from further studies.
  • Modified oligonucleotides described above were further evaluated for potency in non-human primates.
  • NHP non-human primates
  • samples of blood, plasma, serum and urine were collected from all study groups on day 44.
  • the blood samples were collected via femoral venipuncture, 48 hrs post-dosing.
  • the monkeys were fasted overnight prior to blood collection.
  • Approximately 1.5 mL of blood was collected from each animal into tubes without anticoagulant for serum separation.
  • Levels of the various markers were measured using an automated clinical chemistry analyzer (Hitachi Olympus AU400e, Melville, N.Y.).
  • Total urine protein and urine creatinine levels were measured, and the ratio of total urine protein to creatinine (P/C Ratio) was determined.
  • ALT, AST transaminases
  • Albumin Albumin
  • T. Bil total bilirubin
  • BUN blood urea nitrogen
  • Cre creatinine
  • Urine levels of albumin (Alb), creatinine (Cre) and total urine protein were measured, and the ratio of total urine protein to creatinine (P/C ratio) was determined.
  • C-reactive protein which is synthesized in the liver and which serves as a marker of inflammation.
  • CRP C-reactive protein
  • Viscosity of modified oligonucleotide solutions was measured.
  • the viscocity of 935918 is compatible with weekly subcutaneous injection, and the viscosities of both 935918 and 935968 are compatible with IV dosing.
  • Viscosity Compound ID Dose (mg/mL) by weight Viscocity (cP) 690890 300 16.14 935658 300 48.79 935696 300 120.2 935762 300 11.39 935918 100 2.12 935968 300 53.76 882800 100 3.4

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Abstract

The present embodiments provide methods, compounds, and compositions useful for inhibiting IRF4 expression, which may be useful for treating, preventing, or ameliorating a cancer associated with IRF4.

Description

    SEQUENCE LISTING
  • The present application is being filed along with a Sequence Listing in electronic format. The Sequence Listing is provided as a file entitled BIOL0332WOSEQ.txt created Jan. 14, 2019, which is 712 kb in size.
  • The information in the electronic format of the sequence listing is incorporated herein by reference in its entirety.
  • FIELD
  • The present embodiments provide methods, compounds, and compositions useful for inhibiting IRF4 expression, which can be useful for treating, preventing, or ameliorating a cancer associated with IRF4.
  • BACKGROUND
  • Interferon Regulatory Factor 4 (IRF4) is a transcription factor involved in immune responses in normal B and T cells, and is strongly implicated in the development of hematological malignancies, especially multiple mycloma (MM). High IRF4 levels is associated with a poor prognosis of overall survival for MM patients. Upregulation of the cereblon/IRF4 pathway accounts for the failure of lenalidomide treatment, an IMiD approved for MM and B cell malignancies. IRF4 is a component of super enhancer in MM cells in which a positive auto-regulatory loop between the oncogene MYC and IRF4 sustains the survival of MM. IRF4 is also involved in cutaneous anaplastic large cell lymphomas DLBCL, B-cell non-Hodgkin's lymphoma, ALL, adult T cell leukemia/lymphoma (ATLL), and peripheral T cell lymphoma. Despite its role in many cancers, IRF4 is considered an undruggable target by conventional therapeutic approaches.
  • SUMMARY
  • Certain embodiments provided herein are directed to potent and tolerable compounds and compositions useful for inhibiting IRF4 expression, which can be useful for treating, preventing, ameliorating, or slowing progression of cancer associated with IRF4.
  • DETAILED DESCRIPTION
  • It is to be understood that both the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of the embodiments, as claimed. Herein, the use of the singular includes the plural unless specifically stated otherwise. As used herein, the use of “or” means “and/or” unless stated otherwise. Furthermore, the use of the term “including” as well as other forms, such as “includes” and “included”, is not limiting.
  • The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described. All documents, or portions of documents, cited in this application, including, but not limited to, patents, patent applications, articles, books, treatises, and GenBank and NCBI reference sequence records are hereby expressly incorporated by reference for the portions of the document discussed herein, as well as in their entirety.
  • It is understood that the sequence set forth in each SEQ ID NO in the examples contained herein is independent of any modification to a sugar moiety, an internucleoside linkage, or a nucleobase. As such, compounds defined by a SEQ ID NO may comprise, independently, one or more modifications to a sugar moiety, an internucleoside linkage, or a nucleobase. Compounds described by ION number indicate a combination of nucleobase sequence, chemical modification, and motif.
  • Unless otherwise indicated, the following terms have the following meanings:
  • “2′-deoxynucleoside” means a nucleoside comprising 2′-H(H) furanosyl sugar moiety, as found in naturally occurring deoxyribonucleic acids (DNA). In certain embodiments, a 2′-deoxynucleoside may comprise a modified nucleobase or may comprise an RNA nucleobase (uracil).
  • “2′-O-methoxyethyl” (also 2′-MOE and 2′-O(CH2)2—OCH3) refers to an O-methoxy-ethyl modification at the 2′ position of a furanosyl ring. A 2′-O-methoxyethyl modified sugar is a modified sugar.
  • “2′-MOE nucleoside” (also 2′-O-methoxyethyl nucleoside) means a nucleoside comprising a 2′-MOE modified sugar moiety.
  • “2′-substituted nucleoside” or “2-modified nucleoside” means a nucleoside comprising a 2′-substituted or 2′-modified sugar moiety. As used herein, “2′-substituted” or “2-modified” in reference to a sugar moiety means a sugar moiety comprising at least one 2′-substituent group other than H or OH.
  • “3′ target site” refers to the nucleotide of a target nucleic acid which is complementary to the 3′-most nucleotide of a particular compound.
  • “5′ target site” refers to the nucleotide of a target nucleic acid which is complementary to the 5′-most nucleotide of a particular compound.
  • “5-methylcytosine” means a cytosine with a methyl group attached to the 5 position.
  • “About” means within ±10% of a value. For example, if it is stated, “the compounds affected about 70% inhibition of IRF4”, it is implied that IRF4 levels are inhibited within a range of 60% and 80%.
  • “Administration” or “administering” refers to routes of introducing a compound or composition provided herein to an individual to perform its intended function. An example of a route of administration that can be used includes, but is not limited to parenteral administration, such as subcutaneous, intravenous, or intramuscular injection or infusion.
  • “Administered concomitantly” or “co-administration” means administration of two or more compounds in any manner in which the pharmacological effects of both are manifest in the patient. Concomitant administration does not require that both compounds be administered in a single pharmaceutical composition, in the same dosage form, by the same route of administration, or at the same time. The effects of both compounds need not manifest themselves at the same time. The effects need only be overlapping for a period of time and need not be coextensive. Concomitant administration or co-administration encompasses administration in parallel or sequentially.
  • “Amelioration” refers to an improvement or lessening of at least one indicator, sign, or symptom of an associated disease, disorder, or condition. In certain embodiments, amelioration includes a delay or slowing in the progression or severity of one or more indicators of a condition or disease. The progression or severity of indicators may be determined by subjective or objective measures, which are known to those skilled in the art.
  • “Animal” refers to a human or non-human animal, including, but not limited to, mice, rats, rabbits, dogs, cats, pigs, and non-human primates, including, but not limited to, monkeys and chimpanzees.
  • “Antisense activity” means any detectable and/or measurable activity attributable to the hybridization of an antisense compound to its target nucleic acid. In certain embodiments, antisense activity is a decrease in the amount or expression of a target nucleic acid or protein encoded by such target nucleic acid compared to target nucleic acid levels or target protein levels in the absence of the antisense compound to the target.
  • “Antisense compound” means a compound comprising an oligonucleotide and optionally one or more additional features, such as a conjugate group or terminal group. Examples of antisense compounds include single-stranded and double-stranded compounds, such as, oligonucleotides, ribozymes, siRNAs, shRNAs, ssRNAs, and occupancy-based compounds.
  • “Antisense inhibition” means reduction of target nucleic acid levels in the presence of an antisense compound complementary to a target nucleic acid compared to target nucleic acid levels in the absence of the antisense compound.
  • “Antisense mechanisms” are all those mechanisms involving hybridization of a compound with target nucleic acid, wherein the outcome or effect of the hybridization is either target degradation or target occupancy with concomitant stalling of the cellular machinery involving, for example, transcription or splicing.
  • “Antisense oligonucleotide” means an oligonucleotide having a nucleobase sequence that is complementary to a target nucleic acid or region or segment thereof. In certain embodiments, an antisense oligonucleotide is specifically hybridizable to a target nucleic acid or region or segment thereof.
  • “Bicyclic nucleoside” or “BNA” means a nucleoside comprising a bicyclic sugar moiety. “Bicyclic sugar” or “bicyclic sugar moiety” means a modified sugar moiety comprising two rings, wherein the second ring is formed via a bridge connecting two of the atoms in the first ring thereby forming a bicyclic structure. In certain embodiments, the first ring of the bicyclic sugar moiety is a furanosyl moiety. In certain embodiments, the bicyclic sugar moiety does not comprise a furanosyl moiety.
  • “Branching group” means a group of atoms having at least 3 positions that are capable of forming covalent linkages to at least 3 groups. In certain embodiments, a branching group provides a plurality of reactive sites for connecting tethered ligands to an oligonucleotide via a conjugate linker and/or a cleavable moiety.
  • “Cell-targeting moiety” means a conjugate group or portion of a conjugate group that is capable of binding to a particular cell type or particular cell types.
  • “cEt” or “constrained ethyl” means a bicyclic furanosyl sugar moiety comprising a bridge connecting the 4′-carbon and the 2′-carbon, wherein the bridge has the formula: 4′-CH(CH3)—O-2′.
  • “cEt nucleoside” means a nucleoside comprising a cEt modified sugar moiety.
  • “Chemical modification” in a compound describes the substitutions or changes through chemical reaction, of any of the units in the compound relative to the original state of such unit. “Modified nucleoside” means a nucleoside having, independently, a modified sugar moiety and/or modified nucleobase. “Modified oligonucleotide” means an oligonucleotide comprising at least one modified internucleoside linkage, a modified sugar, and/or a modified nucleobase.
  • “Chemically distinct region” refers to a region of a compound that is in some way chemically different than another region of the same compound. For example, a region having 2′-O-methoxyethyl nucleotides is chemically distinct from a region having nucleotides without 2′-O-methoxyethyl modifications.
  • “Chimeric antisense compounds” means antisense compounds that have at least 2 chemically distinct regions, each position having a plurality of subunits.
  • “Chirally enriched population” mean s a plurality of molecules of identical molecular formula, wherein the number or percentage of molecules within the population that contain a particular stereochemical configuration at a particular chiral center is greater than the number or percentage of molecules expected to contain the same particular stereochemical configuration at the same particular chiral center within the population if the particular chiral center were stereorandom. Chirally enriched populations of molecules having multiple chiral centers within each molecule may contain one or more sterorandom chiral centers. In certain embodiments, the molecules are modified oligonucleotides. In certain embodiments, the molecules are compounds comprising modified oligonucleotides.
  • “Cleavable bond” means any chemical bond capable of being split. In certain embodiments, a cleavable bond is selected from among: an amide, a polyamide, an ester, an ether, one or both esters of a phosphodiester, a phosphate ester, a carbamate, a di-sulfide, or a peptide.
  • “Cleavable moiety” means a bond or group of atoms that is cleaved under physiological conditions, for example, inside a cell, an animal, or a human.
  • “Complementary” in reference to an oligonucleotide means the nucleobase sequence of such oligonucleotide or one or more regions thereof matches the nucleobase sequence of another oligonucleotide or nucleic acid or one or more regions thereof when the two nucleobase sequences are aligned in opposing directions. Nucleobase matches or complementary nucleobases, as described herein, are limited to the following pairs: adenine (A) and thymine (T), adenine (A) and uracil (U), cytosine (C) and guanine (G), and 5-methyl cytosine (mC) and guanine (G) unless otherwise specified. Complementary oligonucleotides and/or nucleic acids need not have nucleobase complementarity at each nucleoside and may include one or more nucleobase mismatches. By contrast, “fully complementary” or “100% complementary” in reference to oligonucleotides means that such oligonucleotides have nucleobase matches at each nucleoside without any nucleobase mismatches.
  • “Conjugate group” means a group of atoms that is attached to an oligonucleotide. Conjugate groups include a conjugate moiety and a conjugate linker that attaches the conjugate moiety to the oligonucleotide.
  • “Conjugate linker” means a group of atoms comprising at least one bond that connects a conjugate moiety to an oligonucleotide.
  • “Conjugate moiety” means a group of atoms that is attached to an oligonucleotide via a conjugate linker.
  • “Contiguous” in the context of an oligonucleotide refers to nucleosides, nucleobases, sugar moieties, or internucleoside linkages that are immediately adjacent to each other. For example, “contiguous nucleobases” means nucleobases that are immediately adjacent to each other in a sequence.
  • “Designing” or “Designed to” refer to the process of designing a compound that specifically hybridizes with a selected nucleic acid molecule.
  • “Diluent” means an ingredient in a composition that lacks pharmacological activity, but is pharmaceutically necessary or desirable. For example, the diluent in an injected composition can be a liquid, e.g. saline solution.
  • “Differently modified” means chemical modifications or chemical substituents that are different from one another, including absence of modifications. Thus, for example, a MOE nucleoside and an unmodified DNA nucleoside are “differently modified,” even though the DNA nucleoside is unmodified. Likewise, DNA and RNA are “differently modified,” even though both are naturally-occurring unmodified nucleosides. Nucleosides that are the same but for comprising different nucleobases are not differently modified. For example, a nucleoside comprising a 2′-OMe modified sugar and an unmodified adenine nucleobase and a nucleoside comprising a 2′-OMe modified sugar and an unmodified thymine nucleobase are not differently modified.
  • “Dose” means a specified quantity of a compound or pharmaceutical agent provided in a single administration, or in a specified time period. In certain embodiments, a dose may be administered in two or more boluses, tablets, or injections. For example, in certain embodiments, where subcutaneous administration is desired, the desired dose may require a volume not easily accommodated by a single injection. In such embodiments, two or more injections may be used to achieve the desired dose. In certain embodiments, a dose may be administered in two or more injections to minimize injection site reaction in an individual. In other embodiments, the compound or pharmaceutical agent is administered by infusion over an extended period of time or continuously. Doses may be stated as the amount of pharmaceutical agent per hour, day, week or month.
  • “Dosing regimen” is a combination of doses designed to achieve one or more desired effects.
  • “Double-stranded antisense compound” means an antisense compound comprising two oligomeric compounds that are complementary to each other and form a duplex, and wherein one of the two said oligomeric compounds comprises an oligonucleotide.
  • “Effective amount” means the amount of compound sufficient to effectuate a desired physiological outcome in an individual in need of the compound. The effective amount may vary among individuals depending on the health and physical condition of the individual to be treated, the taxonomic group of the individuals to be treated, the formulation of the composition, assessment of the individual's medical condition, and other relevant factors.
  • “Efficacy” means the ability to produce a desired effect.
  • “Expression” includes all the functions by which a gene's coded information is converted into structures present and operating in a cell. Such structures include, but are not limited to, the products of transcription and translation.
  • “Gapmer” means an oligonucleotide comprising an internal region having a plurality of nucleosides that support RNase H cleavage positioned between external regions having one or more nucleosides, wherein the nucleosides comprising the internal region are chemically distinct from the nucleoside or nucleosides comprising the external regions. The internal region may be referred to as the “gap” and the external regions may be referred to as the “wings.”
  • “Hybridization” means the annealing of oligonucleotides and/or nucleic acids. While not limited to a particular mechanism, the most common mechanism of hybridization involves hydrogen bonding, which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, between complementary nucleobases. In certain embodiments, complementary nucleic acid molecules include, but are not limited to, an antisense compound and a nucleic acid target. In certain embodiments, complementary nucleic acid molecules include, but are not limited to, an oligonucleotide and a nucleic acid target.
  • “Immediately adjacent” means there are no intervening elements between the immediately adjacent elements of the same kind (e.g. no intervening nucleobases between the immediately adjacent nucleobases).
  • “Individual” means a human or non-human animal selected for treatment or therapy.
  • “Inhibiting the expression or activity” refers to a reduction or blockade of the expression or activity relative to the expression of activity in an untreated or control sample and does not necessarily indicate a total elimination of expression or activity.
  • “Internucleoside linkage” means a group or bond that forms a covalent linkage between adjacent nucleosides in an oligonucleotide. “Modified internucleoside linkage” means any internucleoside linkage other than a naturally occurring, phosphate internucleoside linkage Non-phosphate linkages are referred to herein as modified internucleoside linkages.
  • “Lengthened oligonucleotides” are those that have one or more additional nucleosides relative to an oligonucleotide disclosed herein, e.g. a parent oligonucleotide.
  • “Linked nucleosides” means adjacent nucleosides linked together by an internucleoside linkage.
  • “Linker-nucleoside” means a nucleoside that links an oligonucleotide to a conjugate moiety. Linker-nucleosides are located within the conjugate linker of a compound. Linker-nucleosides are not considered part of the oligonucleotide portion of a compound even if they are contiguous with the oligonucleotide.
  • “Mismatch” or “non-complementary” means a nucleobase of a first oligonucleotide that is not complementary to the corresponding nucleobase of a second oligonucleotide or target nucleic acid when the first and second oligonucleotides are aligned. For example, nucleobases including but not limited to a universal nucleobase, inosine, and hypoxanthine, are capable of hybridizing with at least one nucleobase but are still mismatched or non-complementary with respect to nucleobase to which it hybridized. As another example, a nucleobase of a first oligonucleotide that is not capable of hybridizing to the corresponding nucleobase of a second oligonucleotide or target nucleic acid when the first and second oligonucleotides are aligned is a mismatch or non-complementary nucleobase.
  • “Modulating” refers to changing or adjusting a feature in a cell, tissue, organ or organism. For example, modulating IRF4 RNA can mean to increase or decrease the level of IRF4 RNA and/or IRF4 protein in a cell, tissue, organ or organism. A “modulator” effects the change in the cell, tissue, organ or organism. For example, a IRF4 compound can be a modulator that decreases the amount of IRF4 RNA and/or IRF4 protein in a cell, tissue, organ or organism.
  • “MOE” means methoxyethyl.
  • “Monomer” refers to a single unit of an oligomer. Monomers include, but are not limited to, nucleosides and nucleotides.
  • “Motif” means the pattern of unmodified and/or modified sugar moieties, nucleobases, and/or internucleoside linkages, in an oligonucleotide.
  • “Natural” or “naturally occurring” means found in nature.
  • “Non-bicyclic modified sugar” or “non-bicyclic modified sugar moiety” means a modified sugar moiety that comprises a modification, such as a substituent, that does not form a bridge between two atoms of the sugar to form a second ring.
  • “Nucleic acid” refers to molecules composed of monomeric nucleotides. A nucleic acid includes, but is not limited to, ribonucleic acids (RNA), deoxyribonucleic acids (DNA), single-stranded nucleic acids, and double-stranded nucleic acids.
  • “Nucleobase” means a heterocyclic moiety capable of pairing with a base of another nucleic acid. As used herein a “naturally occurring nucleobase” is adenine (A), thymine (T), cytosine (C), uracil (U), and guanine (G). A “modified nucleobase” is a naturally occurring nucleobase that is chemically modified. A “universal base” or “universal nucleobase” is a nucleobase other than a naturally occurring nucleobase and modified nucleobase, and is capable of pairing with any nucleobase.
  • “Nucleobase sequence” means the order of contiguous nucleobases in a nucleic acid or oligonucleotide independent of any sugar or internucleoside linkage.
  • “Nucleoside” means a compound comprising a nucleobase and a sugar moiety. The nucleobase and sugar moiety are each, independently, unmodified or modified. “Modified nucleoside” means a nucleoside comprising a modified nucleobase and/or a modified sugar moiety. Modified nucleosides include abasic nucleosides, which lack a nucleobase.
  • “Oligomeric compound” means a compound comprising a single oligonucleotide and optionally one or more additional features, such as a conjugate group or terminal group.
  • “Oligonucleotide” means a polymer of linked nucleosides each of which can be modified or unmodified, independent one from another. Unless otherwise indicated, oligonucleotides consist of 8-80 linked nucleosides. “Modified oligonucleotide” means an oligonucleotide, wherein at least one sugar, nucleobase, or internucleoside linkage is modified. “Unmodified oligonucleotide” means an oligonucleotide that does not comprise any sugar, nucleobase, or internucleoside modification.
  • “Parent oligonucleotide” means an oligonucleotide whose sequence is used as the basis of design for more oligonucleotides of similar sequence but with different lengths, motifs, and/or chemistries. The newly designed oligonucleotides may have the same or overlapping sequence as the parent oligonucleotide.
  • “Parenteral administration” means administration through injection or infusion. Parenteral administration includes subcutaneous administration, intravenous administration, intramuscular administration, intraarterial administration, intraperitoneal administration, or intracranial administration, e.g. intrathecal or intracerebroventricular administration.
  • “Pharmaceutically acceptable carrier or diluent” means any substance suitable for use in administering to an individual. For example, a pharmaceutically acceptable carrier can be a sterile aqueous solution, such as PBS or water-for-injection.
  • “Pharmaceutically acceptable salts” means physiologically and pharmaceutically acceptable salts of compounds, such as oligomeric compounds or oligonucleotides, i.e., salts that retain the desired biological activity of the parent compound and do not impart undesired toxicological effects thereto.
  • “Pharmaceutical agent” means a compound that provides a therapeutic benefit when administered to an individual.
  • “Pharmaceutical composition” means a mixture of substances suitable for administering to an individual. For example, a pharmaceutical composition may comprise one or more compounds or salt thereof and a sterile aqueous solution.
  • “Phosphorothioate linkage” means a modified phosphate linkage in which one of the non-bridging oxygen atoms is replaced with a sulfur atom. A phosphorothioate internucleoside linkage is a modified internucleoside linkage.
  • “Phosphorus moiety” means a group of atoms comprising a phosphorus atom. In certain embodiments, a phosphorus moiety comprises a mono-, di-, or tri-phosphate, or phosphorothioate.
  • “Portion” means a defined number of contiguous (i.e., linked) nucleobases of a nucleic acid. In certain embodiments, a portion is a defined number of contiguous nucleobases of a target nucleic acid. In certain embodiments, a portion is a defined number of contiguous nucleobases of an oligomeric compound.
  • “Prevent” refers to delaying or forestalling the onset, development or progression of a disease, disorder, or condition for a period of time from minutes to indefinitely.
  • “Prodrug” means a compound in a form outside the body which, when administered to an individual, is metabolized to another form within the body or cells thereof. In certain embodiments, the metabolized form is the active, or more active, form of the compound (e.g., drug). Typically conversion of a prodrug within the body is facilitated by the action of an enzyme(s) (e.g., endogenous or viral enzyme) or chemical(s) present in cells or tissues, and/or by physiologic conditions.
  • “Reduce” means to bring down to a smaller extent, size, amount, or number.
  • “RefSeq No.” is a unique combination of letters and numbers assigned to a sequence to indicate the sequence is for a particular target transcript (e.g., target gene). Such sequence and information about the target gene (collectively, the gene record) can be found in a genetic sequence database. Genetic sequence databases include the NCBI Reference Sequence database, GenBank, the European Nucleotide Archive, and the DNA Data Bank of Japan (the latter three forming the International Nucleotide Sequence Database Collaboration or INSDC).
  • “Region” is defined as a portion of the target nucleic acid having at least one identifiable structure, function, or characteristic.
  • “RNAi compound” means an antisense compound that acts, at least in part, through RISC or Ago2, but not through RNase H, to modulate a target nucleic acid and/or protein encoded by a target nucleic acid. RNAi compounds include, but are not limited to double-stranded siRNA, single-stranded RNA (ssRNA), and microRNA, including microRNA mimics.
  • “Segments” are defined as smaller or sub-portions of regions within a nucleic acid.
  • “Side effects” means physiological disease and/or conditions attributable to a treatment other than the desired effects. In certain embodiments, side effects include injection site reactions, liver function test abnormalities, renal function abnormalities, liver toxicity, renal toxicity, central nervous system abnormalities, myopathies, and malaise. For example, increased aminotransferase levels in serum may indicate liver toxicity or liver function abnormality. For example, increased bilirubin may indicate liver toxicity or liver function abnormality.
  • “Single-stranded” in reference to a compound means the compound has only one oligonucleotide. “Self-complementary” means an oligonucleotide that at least partially hybridizes to itself. A compound consisting of one oligonucleotide, wherein the oligonucleotide of the compound is self-complementary, is a single-stranded compound. A single-stranded compound may be capable of binding to a complementary compound to form a duplex.
  • “Sites” are defined as unique nucleobase positions within a target nucleic acid.
  • “Specifically hybridizable” refers to an oligonucleotide having a sufficient degree of complementarity between the oligonucleotide and a target nucleic acid to induce a desired effect, while exhibiting minimal or no effects on non-target nucleic acids. In certain embodiments, specific hybridization occurs under physiological conditions.
  • “Specifically inhibit” with reference to a target nucleic acid means to reduce or block expression of the target nucleic acid while exhibiting fewer, minimal, or no effects on non-target nucleic acids. Reduction does not necessarily indicate a total elimination of the target nucleic acid's expression.
  • “Standard cell assay” means assay(s) described in the Examples and reasonable variations thereof.
  • “Standard in vivo experiment” means the procedure(s) described in the Example(s) and reasonable variations thereof.
  • “Stereorandom chiral center” in the context of a population of molecules of identical molecular formula means a chiral center having a random stereochemical configuration. For example, in a population of molecules comprising a stereorandom chiral center, the number of molecules having the (S) configuration of the stereorandom chiral center may be but is not necessarily the same as the number of molecules having the (R) configuration of the stereorandom chiral center. The stereochemical configuration of a chiral center is considered random when it is the result of a synthetic method that is not designed to control the stereochemical configuration. In certain embodiments, a stereorandom chiral center is a stereorandom phosphorothioate internucleoside linkage.
  • “Sugar moiety” means an unmodified sugar moiety or a modified sugar moiety. “Unmodified sugar moiety” or “unmodified sugar” means a 2′-OH(H) furanosyl moiety, as found in RNA (an “unmodified RNA sugar moiety”), or a 2′-H(H) moiety, as found in DNA (an “unmodified DNA sugar moiety”). Unmodified sugar moieties have one hydrogen at each of the 1′, 3′, and 4′ positions, an oxygen at the 3′ position, and two hydrogens at the 5′ position. “Modified sugar moiety” or “modified sugar” means a modified furanosyl sugar moiety or a sugar surrogate. “Modified furanosyl sugar moiety” means a furanosyl sugar comprising a non-hydrogen substituent in place of at least one hydrogen of an unmodified sugar moiety. In certain embodiments, a modified furanosyl sugar moiety is a 2′-substituted sugar moiety. Such modified furanosyl sugar moieties include bicyclic sugars and non-bicyclic sugars.
  • “Sugar surrogate” means a modified sugar moiety having other than a furanosyl moiety that can link a nucleobase to another group, such as an internucleoside linkage, conjugate group, or terminal group in an oligonucleotide. Modified nucleosides comprising sugar surrogates can be incorporated into one or more positions within an oligonucleotide and such oligonucleotides are capable of hybridizing to complementary compounds or nucleic acids.
  • “Synergy” or “synergize” refers to an effect of a combination that is greater than additive of the effects of each component alone at the same doses.
  • “IRF4” means any nucleic acid or protein of IRF4. “IRF4 nucleic acid” means any nucleic acid encoding TRF4. For example, in certain embodiments, a TRF4 nucleic acid includes a DNA sequence encoding IRF4, an RNA sequence transcribed from DNA encoding IRF4 (including genomic DNA comprising introns and exons), and an mRNA sequence encoding IRF4. “IRF4 mRNA” means an mRNA encoding a IRF4 protein. The target may be referred to in either upper or lower case.
  • “IRF4 specific inhibitor” refers to any agent capable of specifically inhibiting IRF4 RNA and/or IRF4 protein expression or activity at the molecular level. For example, IRF4 specific inhibitors include nucleic acids (including antisense compounds), peptides, antibodies, small molecules, and other agents capable of inhibiting the expression of IRF4 RNA and/or IRF4 protein.
  • “Target gene” refers to a gene encoding a target.
  • “Targeting” means the specific hybridization of a compound to a target nucleic acid in order to induce a desired effect.
  • “Target nucleic acid,” “target RNA,” “target RNA transcript” and “nucleic acid target” all mean a nucleic acid capable of being targeted by compounds described herein.
  • “Target region” means a portion of a target nucleic acid to which one or more compounds is targeted.
  • “Target segment” means the sequence of nucleotides of a target nucleic acid to which a compound is targeted. “5′ target site” refers to the 5′-most nucleotide of a target segment. “3′ target site” refers to the 3′-most nucleotide of a target segment.
  • “Terminal group” means a chemical group or group of atoms that is covalently linked to a terminus of an oligonucleotide.
  • “Therapeutically effective amount” means an amount of a compound, pharmaceutical agent, or composition that provides a therapeutic benefit to an individual.
  • “Treat” refers to administering a compound or pharmaceutical composition to an animal in order to effect an alteration or improvement of a disease, disorder, or condition in the animal.
  • CERTAIN EMBODIMENTS
  • Certain embodiments provide methods, compounds and compositions for inhibiting IRF4 expression.
  • Certain embodiments provide compounds targeted to a IRF4 nucleic acid. In certain embodiments, the IRF4 nucleic acid has the sequence set forth in RefSeq or GENBANK Accession No. NM_002460.3 or NT_034880.3_TRUNC_328000_354000 (incorporated by reference, disclosed herein as SEQ ID NO: 1 and SEQ ID NO: 2, respectively). In certain embodiments, the compound is an antisense compound or oligomeric compound. In certain embodiments, the compound is single-stranded. In certain embodiments, the compound is double-stranded.
  • Certain embodiments provide a compound comprising a modified oligonucleotide 8 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 8 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383. In certain embodiments, the compound is an antisense compound or oligomeric compound. In certain embodiments, the compound is single-stranded. In certain embodiments, the compound is double-stranded. In certain embodiments, the modified oligonucleotide is 10 to 30 linked nucleosides in length.
  • Certain embodiments provide a compound comprising a modified oligonucleotide 9 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 9 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383. In certain embodiments, the compound is an antisense compound or oligomeric compound. In certain embodiments, the compound is single-stranded. In certain embodiments, the compound is double-stranded. In certain embodiments, the modified oligonucleotide is 10 to 30 linked nucleosides in length.
  • Certain embodiments provide a compound comprising a modified oligonucleotide 10 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 10 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383. In certain embodiments, the compound is an antisense compound or oligomeric compound. In certain embodiments, the compound is single-stranded. In certain embodiments, the compound is double-stranded. In certain embodiments, the modified oligonucleotide is 10 to 30 linked nucleosides in length.
  • Certain embodiments provide a compound comprising a modified oligonucleotide 11 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 11 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383. In certain embodiments, the compound is an antisense compound or oligomeric compound. In certain embodiments, the compound is single-stranded. In certain embodiments, the compound is double-stranded. In certain embodiments, the modified oligonucleotide is 11 to 30 linked nucleosides in length.
  • Certain embodiments provide a compound comprising a modified oligonucleotide 12 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 12 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383. In certain embodiments, the compound is an antisense compound or oligomeric compound. In certain embodiments, the compound is single-stranded. In certain embodiments, the compound is double-stranded. In certain embodiments, the modified oligonucleotide is 12 to 30 linked nucleosides in length.
  • Certain embodiments provide a compound comprising a modified oligonucleotide 16 to 80 linked nucleosides in length and having a nucleobase sequence comprising the nucleobase sequence of any one of SEQ ID NOs: 3-3383. In certain embodiments, the compound is an antisense compound or oligomeric compound. In certain embodiments, the compound is single-stranded. In certain embodiments, the compound is double-stranded. In certain embodiments, the modified oligonucleotide is 16 to 30 linked nucleosides in length.
  • Certain embodiments provide a compound comprising a modified oligonucleotide consisting of the nucleobase sequence of any one of SEQ ID NOs: 3-3383. In certain embodiments, the compound is an antisense compound or oligomeric compound. In certain embodiments, the compound is single-stranded. In certain embodiments, the compound is double-stranded.
  • In certain embodiments, a compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having at least an 8, 9, 10, 11, 12, 13, 14, 15, or 16 contiguous nucleobase portion complementary to an equal length portion within the 3′UTR of SEQ ID NO: 1. In certain embodiments, the 3′UTR corresponds to nucleotides 1483 to 5332 of SEQ ID NO: 1. In certain embodiments, a compound comprises a modified oligonucleotide 10 to 30 linked nucleosides in length having a nucleobase sequence at least 85%, at least 90%, at least 95%, or 100% complementary across its entire length to a nucleobase sequence within the 3′UTR of SEQ ID NO: 1. In certain embodiments, the 3′UTR corresponds to nucleotides 1483 to 5332 of SEQ ID NO: 1. In certain embodiments, a compound comprises a modified oligonucleotide 16 to 30 linked nucleosides in length having a nucleobase sequence at least 85%, at least 90%, at least 95%, or 100% complementary across its entire length to a nucleobase sequence within the 3′UTR of SEQ ID NO: 1. In certain embodiments, the 3′UTR corresponds to nucleotides 1483 to 5332 of SEQ ID NO: 1.
  • In certain embodiments, a compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having at least an 8, 9, 10, 11, 12, 13, 14, 15, or 16 contiguous nucleobase portion complementary to an equal length portion within nucleotides 4227-4244, 4227-4242, 4228-4243, or 4229-4244 of SEQ ID NO: 1. In certain embodiments, the modified oligonucleotide is 10 to 30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 to 30 linked nucleosides in length.
  • In certain embodiments, a compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having at least an 8, 9, 10, 11, 12, 13, 14, 15, or 16 contiguous nucleobase portion complementary to an equal length portion within nucleotides 9667-9682, 11411-11426, or 18090-18105 of SEQ ID NO: 2. In certain embodiments, the modified oligonucleotide is 10 to 30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 to 30 linked nucleosides in length.
  • In certain embodiments, a compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and complementary within nucleotides 4227-4244, 4227-4242, 4228-4243, or 4229-4244 of SEQ ID NO: 1. In certain embodiments, the modified oligonucleotide is 10 to 30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 to 30 linked nucleosides in length.
  • In certain embodiments, a compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and complementary within nucleotides 9667-9682, 11411-11426, or 18090-18105 of SEQ ID NO: 2. In certain embodiments, the modified oligonucleotide is 10 to 30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 to 30 linked nucleosides in length.
  • In certain embodiments, a compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least an 8, 9, 10, 11, 12, 13, 14, 15, or 16 contiguous nucleobase portion any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303. In certain embodiments, the modified oligonucleotide is 10 to 30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 to 30 linked nucleosides in length.
  • In certain embodiments, a compound comprises a modified oligonucleotide 16 to 80 linked nucleosides in length and having a nucleobase sequence comprising any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303. In certain embodiments, the modified oligonucleotide is 16 to 30 linked nucleosides in length.
  • In certain embodiments, a compound comprises a modified oligonucleotide 16 linked nucleosides in length having a nucleobase sequence consisting of any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • In certain embodiments, a compound targeted to IRF4 is ION 935918. Out of over 3,000 compounds that were screened as described in the Examples section below, ION 690890, 935658, 935696, 935762, 935918, 935968, 882800, 1012795, 1014095, and 1014834 emerged as the top lead compounds. In particular, ION 935918 exhibited the best combination of properties in terms of potency and tolerability out of over 3,000 compounds.
  • In certain embodiments, any of the foregoing modified oligonucleotides comprises at least one modified internucleoside linkage, at least one modified sugar, and/or at least one modified nucleobase.
  • In certain embodiments, any of the foregoing modified oligonucleotides comprises at least one modified sugar. In certain embodiments, at least one modified sugar comprises a 2′-O-methoxyethyl group. In certain embodiments, at least one modified sugar is a bicyclic sugar, such as a 4′-CH(CH3)—O-2′ group, a 4′-CH2—O-2′ group, or a 4′-(CH2)2—O-2′ group.
  • In certain embodiments, the modified oligonucleotide comprises at least one modified internucleoside linkage, such as a phosphorothioate internucleoside linkage.
  • In certain embodiments, any of the foregoing modified oligonucleotides comprises at least one modified nucleobase, such as 5-methylcytosine.
  • In certain embodiments, any of the foregoing modified oligonucleotides comprises:
      • a gap segment consisting of linked deoxynucleosides;
      • a 5′ wing segment consisting of linked nucleosides; and
      • a 3′ wing segment consisting of linked nucleosides;
  • wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment and wherein each nucleoside of each wing segment comprises a modified sugar. In certain embodiments, the modified oligonucleotide is 16 to 80 linked nucleosides in length having a nucleobase sequence comprising the sequence recited in any one of SEQ ID NO: 2021, 560, 559, 1330, 1540, or 3303. In certain embodiments, the modified oligonucleotide is 16 to 30 linked nucleosides in length having a nucleobase sequence comprising the sequence recited in any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length having a nucleobase sequence consisting of the sequence recited in any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303.
  • In certain embodiments, a compound comprises or consists of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in any one of SEQ ID NOs: 3-3383, wherein the modified oligonucleotide comprises:
      • a gap segment consisting of linked deoxynucleosides;
      • a 5′ wing segment consisting of linked nucleosides; and
      • a 3′ wing segment consisting of linked nucleosides;
  • wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment and wherein each nucleoside of each wing segment comprises a modified sugar. In certain embodiments, the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • In certain embodiments, a compound comprises or consists of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303, wherein the modified oligonucleotide comprises:
      • a gap segment consisting of linked deoxynucleosides;
      • a 5′ wing segment consisting of linked nucleosides; and
      • a 3′ wing segment consisting of linked nucleosides;
  • wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment and wherein each nucleoside of each wing segment comprises a modified sugar. In certain embodiments, the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • In certain embodiments, a compound comprises or consists of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in any one of SEQ ID NOs: 1330 or 3303, wherein the modified oligonucleotide comprises:
  • a gap segment consisting of ten linked deoxynucleosides;
  • a 5′ wing segment consisting of three linked nucleosides; and
  • a 3′ wing segment consisting of three linked nucleosides;
  • wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of each wing segment comprises a cEt nucleoside; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine. In certain embodiments, the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • In certain embodiments, a compound comprises or consists of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in any one of SEQ ID NOs: 559 or 560, wherein the modified oligonucleotide comprises:
  • a gap segment consisting of ten linked deoxynucleosides;
  • a 5′ wing segment consisting of one linked nucleoside; and
  • a 3′ wing segment consisting of five linked nucleosides;
  • wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein the 5′ wing segment comprises a cEt nucleoside; wherein the 3′ wing segment comprises a cEt nucleoside, a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, a 2′-O-methoxyethyl nucleoside, and a cEt nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine. In certain embodiments, the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • In certain embodiments, a compound comprises or consists of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in any one of SEQ ID NOs: 1330 or 2021, wherein the modified oligonucleotide comprises:
  • a gap segment consisting of ten linked deoxynucleosides;
  • a 5′ wing segment consisting of two linked nucleosides; and
  • a 3′ wing segment consisting of four linked nucleosides;
  • wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of the 5′ wing segment comprises a cEt nucleoside; wherein the 3′ wing segment comprises a cEt nucleoside, a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, and a 2′-O-methoxyethyl nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine. In certain embodiments, the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • In certain embodiments, a compound comprises or consists of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in SEQ ID NO: 560, wherein the modified oligonucleotide comprises:
  • a gap segment consisting of nine linked deoxynucleosides;
  • a 5′ wing segment consisting of two linked nucleosides; and
  • a 3′ wing segment consisting of five linked nucleosides;
  • wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of the 5′ wing segment comprises a cEt nucleoside; wherein the 3′ wing segment comprises a cEt nucleoside, a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, a 2′-O-methoxyethyl nucleoside, and a cEt nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine. In certain embodiments, the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • In certain embodiments, a compound comprises or consists of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in SEQ ID NOs: 2021, wherein the modified oligonucleotide comprises:
  • a gap segment consisting of nine linked deoxynucleosides;
  • a 5′ wing segment consisting of two linked nucleosides; and
  • a 3′ wing segment consisting of five linked nucleosides;
  • wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of the 5′ wing segment comprises a cEt nucleoside; wherein the 3′ wing segment comprises a 2′-O-methoxyethyl nucleoside, a 2′-O-methoxyethyl nucleoside, a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, and a cEt nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine. In certain embodiments, the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • In certain embodiments, a compound comprises or consists of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in SEQ ID NOs: 1540, wherein the modified oligonucleotide comprises:
  • a gap segment consisting of nine linked deoxynucleosides;
  • a 5′ wing segment consisting of two linked nucleosides; and
  • a 3′ wing segment consisting of five linked nucleosides;
  • wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of the 5′ wing segment comprises a cEt nucleoside; wherein the 3′ wing segment comprises a 2′-O-methoxyethyl nucleoside, a 2′-O-methoxyethyl nucleoside, a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, and a cEt nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine. In certain embodiments, the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • In certain embodiments, a compound comprises or consists of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in SEQ ID NOs: 560, wherein the modified oligonucleotide comprises:
  • a gap segment consisting of nine linked deoxynucleosides;
  • a 5′ wing segment consisting of two linked nucleosides; and
  • a 3′ wing segment consisting of five linked nucleosides;
  • wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of the 5′ wing segment comprises a cEt nucleoside; wherein the 3′ wing segment comprises a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, and a 2′-O-methoxyethyl nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine. In certain embodiments, the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • In certain embodiments, a compound comprises or consists of ION 935918 or salt thereof, having the following chemical structure:
  • Figure US20220241320A1-20220804-C00001
  • In certain embodiments, a compound comprises or consists of the sodium salt of ION 935918, having the following chemical structure:
  • Figure US20220241320A1-20220804-C00002
  • In certain embodiments, a compound comprises or consists of ION 935968 or salt thereof, having the following chemical structure:
  • Figure US20220241320A1-20220804-C00003
  • In certain embodiments, a compound comprises or consists of the sodium salt of ION 935968, having the following chemical structure:
  • Figure US20220241320A1-20220804-C00004
  • In any of the foregoing embodiments, the compound or oligonucleotide can be at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% complementary to a nucleic acid encoding IRF4.
  • In any of the foregoing embodiments, the compound can be single-stranded. In certain embodiments, the compound comprises deoxyribonucleotides. In certain embodiments, the compound is double-stranded. In certain embodiments, the compound is double-stranded and comprises ribonucleotides. In any of the foregoing embodiments, the compound can be an antisense compound or oligomeric compound.
  • In any of the foregoing embodiments, the compound can be 8 to 80, 10 to 30, 12 to 50, 13 to 30, 13 to 50, 14 to 30, 14 to 50, 15 to 30, 15 to 50, 16 to 30, 16 to 50, 17 to 30, 17 to 50, 18 to 22, 18 to 24, 18 to 30, 18 to 50, 19 to 22, 19 to 30, 19 to 50, or 20 to 30 linked nucleosides in length. In certain embodiments, the compound comprises or consists of an oligonucleotide.
  • In certain embodiments, compounds or compositions provided herein comprise a salt of the modified oligonucleotide. In certain embodiments, the salt is a sodium salt. In certain embodiments, the salt is a potassium salt.
  • In certain embodiments, the compounds or compositions as described herein are highly tolerable as demonstrated by having at least one of an increase an alanine transaminase (ALT) or aspartate transaminase (AST) value of no more than 4 fold, 3 fold, or 2 fold over saline treated animals or an increase in liver, spleen, or kidney weight of no more than 30%, 20%, 15%, 12%, 10%, 5%, or 2% compared to control treated animals. In certain embodiments, the compounds or compositions as described herein are highly tolerable as demonstrated by having no increase of ALT or AST over control treated animals. In certain embodiments, the compounds or compositions as described herein are highly tolerable as demonstrated by having no increase in liver, spleen, or kidney weight over control animals.
  • Certain embodiments provide a composition comprising the compound of any of the aforementioned embodiments or salt thereof and at least one of a pharmaceutically acceptable carrier or diluent. In certain embodiments, the composition has a viscosity less than about 40 centipoise (cP), less than about 30 centipose (cP), less than about 20 centipose (cP), less than about 15 centipose (cP), or less than about 10 centipose (cP). In certain embodiments, the composition having any of the aforementioned viscosities comprises a compound provided herein at a concentration of about 100 mg/mL, about 125 mg/mL, about 150 mg/mL, about 175 mg/mL, about 200 mg/mL, about 225 mg/mL, about 250 mg/mL, about 275 mg/mL, or about 300 mg/mL. In certain embodiments, the composition having any of the aforementioned viscosities and/or compound concentrations has a temperature of room temperature or about 20° C., about 21° C., about 22° C., about 23° C., about 24° C., about 25° C., about 26° C., about 27° C., about 28° C., about 29° C., or about 30° C.
  • Certain Indications
  • Certain embodiments provided herein relate to methods of inhibiting IRF4 expression, which can be useful for treating, preventing, or ameliorating a cancer associated with IRF4 in an individual, by administration of a compound that targets IRF4. In certain embodiments, the compound can be a IRF4 specific inhibitor. In certain embodiments, the compound can be an antisense compound, oligomeric compound, or oligonucleotide targeted to IRF4.
  • Examples of cancers associated with IRF4 treatable, preventable, and/or ameliorable with the methods provided herein include blood cancer, myeloma, multiple myeloma (MM), B cell malignancies, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia. In certain embodiments, the B-cell lymphoma is a non-Hodgkin's B-cell lymphoma. Examples of non-Hodgkin's B-cell lymphoma of certain embodiments that can be treated with compounds provided herein include, but are not limited to, diffuse large B cell lymphoma (DLBCL), activated B-cell lymphoma (ABC-DLBCL), germinal center B-cell lymphoma (GCB DLBCL), follicular lymphoma, mucosa-associated lymphatic tissue lymphoma (MALT), small cell lymphocytic lymphoma, chronic lymphocytic leukemia, mantle cell lymphoma (MCL), Burkitt lymphoma, mediastinal large B cell lymphoma, Waldenstrom macroglobulinemia, nodal marginal zone B cell lymphoma (NMZL), splenic marginal zone lymphoma (SMZL), intravascular large B-cell lymphoma, primary effusion lymphoma, and lymphomatoid granulomatosis. In certain embodiments, the T-cell lymphoma that can be treated with compounds provided herein include, but are not limited to, peripheral T-cell lymphoma, adult T cell leukemia/lymphoma (ATLL), and anaplastic large cell lymphoma (ALCL). In certain embodiments, the leukemia that can be treated with compounds provided herein includes, but is not limited to, acute lymphocytic leukemia (ALL).
  • In certain embodiments, a method of treating, preventing, or ameliorating a cancer associated with IRF4 in an individual comprises administering to the individual a compound comprising a IRF4 specific inhibitor, thereby treating, preventing, or ameliorating the cancer. In certain embodiments, the compound comprises an antisense compound targeted to IRF4. In certain embodiments, the compound comprises an oligonucleotide targeted to IRF4. In certain embodiments, a compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 8 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383. In certain embodiments, a compound comprises a modified oligonucleotide 16 to 80 linked nucleosides in length and having a nucleobase sequence comprising the nucleobase sequence of any one of SEQ ID NOs: 3-3383. In certain embodiments, a compound comprises a modified oligonucleotide consisting of the nucleobase sequence of any one of SEQ ID NOs: 3-3383. In certain embodiments, a compound comprises a modified oligonucleotide 16 to 80 linked nucleosides in length having a nucleobase sequence comprising any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303. In certain embodiments, a compound comprises a modified oligonucleotide having a nucleobase sequence consisting of any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303. In any of the foregoing embodiments, the modified oligonucleotide can be 10 to 30 linked nucleosides in length. In certain embodiments, the compound is ION 690890, 935658, 935696, 935762, 935918, 935968, 882800, 1012795, 1014095, and 1014834. In any of the foregoing embodiments, the compound can be single-stranded or double-stranded. In any of the foregoing embodiments, the compound can be an antisense compound or oligomeric compound. In certain embodiments, the compound is administered to the individual parenterally. In certain embodiments, administering the compound inhibits or reduces cancer cell proliferation, tumor growth, or metastasis.
  • In certain embodiments, a method of treating or ameliorating caner comprises administering to the individual a compound comprising a IRF4 specific inhibitor, thereby treating or ameliorating the cancer. In certain embodiments, the cancer is a blood cancer, myeloma, multiple myeloma (MM), B cell malignancy, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia. In certain embodiments, the B-cell lymphoma is a non-Hodgkin's B-cell lymphoma. Examples of non-Hodgkin's B-cell lymphoma of certain embodiments that can be treated with compounds provided herein include, but are not limited to, diffuse large B cell lymphoma (DLBCL), activated B-cell lymphoma (ABC-DLBCL), germinal center B-cell lymphoma (GCB DLBCL), follicular lymphoma, mucosa-associated lymphatic tissue lymphoma (MALT), small cell lymphocytic lymphoma, chronic lymphocytic leukemia, mantle cell lymphoma (MCL), Burkitt lymphoma, mediastinal large B cell lymphoma, Waldenström macroglobulinemia, nodal marginal zone B cell lymphoma (NMZL), splenic marginal zone lymphoma (SMZL), intravascular large B-cell lymphoma, primary effusion lymphoma, and lymphomatoid granulomatosis. In certain embodiments, the T-cell lymphoma that can be treated with compounds provided herein include, but are not limited to, peripheral T-cell lymphoma, adult T cell leukemia/lymphoma (ATLL), and anaplastic large cell lymphoma (ALCL). In certain embodiments, the leukemia that can be treated with compounds provided herein includes, but is not limited to, acute lymphocytic leukemia (ALL). In certain embodiments, the compound comprises an antisense compound targeted to IRF4. In certain embodiments, the compound comprises an oligonucleotide targeted to IRF4. In certain embodiments, the compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 8 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a modified oligonucleotide 16 to 80 linked nucleosides in length and having a nucleobase sequence comprising the nucleobase sequence of any one of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a modified oligonucleotide consisting of the nucleobase sequence of any one of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a modified oligonucleotide of 16 to 80 linked nucleosides in length having a nucleobase sequence comprising any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303. In certain embodiments, the compound comprises a modified oligonucleotide having a nucleobase sequence consisting of any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303. In any of the foregoing embodiments, the modified oligonucleotide can be 10 to 30 linked nucleosides in length. In certain embodiments, the compound is ION 690890, 935658, 935696, 935762, 935918, 935968, 882800, 1012795, 1014095, and 1014834. In any of the foregoing embodiments, the compound can be single-stranded or double-stranded. In any of the foregoing embodiments, the compound can be an antisense compound or oligomeric compound. In certain embodiments, the compound is administered to the individual parenterally. In certain embodiments, administering the compound inhibits or reduces cancer cell proliferation, tumor growth, or metastasis. In certain embodiments, the individual is identified as having or at risk of having a cancer associated with IRF4.
  • In certain embodiments, a method of inhibiting expression of IRF4 in an individual having, or at risk of having, a cancer associated with IRF4 comprises administering to the individual a compound comprising a IRF4 specific inhibitor, thereby inhibiting expression of IRF4 in the individual. In certain embodiments, administering the compound inhibits expression of IRF4 in the bone marrow, lymphoid tissue, or lymph node.
  • In certain embodiments, the individual has, or is at risk of having blood cancer, myeloma, multiple myeloma (MM), B cell malignancies, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia. In certain embodiments, the B-cell lymphoma is a non-Hodgkin's B-cell lymphoma. Examples of non-Hodgkin's B-cell lymphoma of certain embodiments that can be treated with compounds provided herein include, but are not limited to, diffuse large B cell lymphoma (DLBCL), activated B-cell lymphoma (ABC-DLBCL), germinal center B-cell lymphoma (GCB DLBCL), follicular lymphoma, mucosa-associated lymphatic tissue lymphoma (MALT), small cell lymphocytic lymphoma, chronic lymphocytic leukemia, mantle cell lymphoma (MCL), Burkitt lymphoma, mediastinal large B cell lymphoma, Waldenstrom macroglobulinemia, nodal marginal zone B cell lymphoma (NMZL), splenic marginal zone lymphoma (SMZL), intravascular large B-cell lymphoma, primary effusion lymphoma, and lymphomatoid granulomatosis. In certain embodiments, the T-cell lymphoma that can be treated with compounds provided herein include, but are not limited to, peripheral T-cell lymphoma, adult T cell leukemia/lymphoma (ATLL), and anaplastic large cell lymphoma (ALCL). In certain embodiments, the leukemia that can be treated with compounds provided herein includes, but is not limited to, acute lymphocytic leukemia (ALL). In certain embodiments, the compound comprises an antisense compound targeted to IRF4. In certain embodiments, the compound comprises an oligonucleotide targeted to IRF4. In certain embodiments, the compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 8 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a modified oligonucleotide 16 to 80 linked nucleosides in length and having a nucleobase sequence comprising the nucleobase sequence of any one of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a modified oligonucleotide consisting of the nucleobase sequence of any one of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a modified oligonucleotide of 16 to 80 linked nucleosides in length having a nucleobase sequence comprising any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303. In certain embodiments, the compound comprises a modified oligonucleotide having a nucleobase sequence consisting of any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303. In any of the foregoing embodiments, the modified oligonucleotide can be 10 to 30 linked nucleosides in length. In certain embodiments, the compound is ION 690890, 935658, 935696, 935762, 935918, 935968, 882800, 1012795, 1014095, and 1014834. In any of the foregoing embodiments, the compound can be single-stranded or double-stranded. In any of the foregoing embodiments, the compound can be an antisense compound or oligomeric compound. In certain embodiments, the compound is administered to the individual parenterally. In certain embodiments, administering the compound inhibits or reduces cancer cell proliferation, tumor growth, or metastasis. In certain embodiments, the individual is identified as having or at risk of having a cancer associated with IRF4.
  • In certain embodiments, a method of inhibiting expression of IRF4 in a cell comprises contacting the cell with a compound comprising a IRF4 specific inhibitor, thereby inhibiting expression of IRF4 in the cell. In certain embodiments, the cell is a cancer cell. In certain embodiments, the cell is a bone marrow, lymphoid tissue, or lymph node cell. In certain embodiments, the cell is in the bone marrow, lymphoid tissue, or lymph node. In certain embodiments, the cell is in the bone marrow, lymphoid tissue, or lymph node of an individual who has, or is at risk of having cancer, such as blood cancer, myeloma, multiple myeloma (MM), B cell malignancies, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia. In certain embodiments, the compound comprises an antisense compound targeted to IRF4. In certain embodiments, the compound comprises an oligonucleotide targeted to IRF4. In certain embodiments, the compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 8 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a modified oligonucleotide 16 to 80 linked nucleosides in length and having a nucleobase sequence comprising the nucleobase sequence of any one of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a modified oligonucleotide consisting of the nucleobase sequence of any one of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a modified oligonucleotide of 16 to 80 linked nucleosides in length having a nucleobase sequence comprising any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303. In certain embodiments, the compound comprises a modified oligonucleotide having a nucleobase sequence consisting of any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303. In any of the foregoing embodiments, the modified oligonucleotide can be 10 to 30 linked nucleosides in length. In certain embodiments, the compound is ION 690890, 935658, 935696, 935762, 935918, 935968, 882800, 1012795, 1014095, and 1014834. In any of the foregoing embodiments, the compound can be single-stranded or double-stranded. In any of the foregoing embodiments, the compound can be an antisense compound or oligomeric compound.
  • In certain embodiments, a method of reducing or inhibiting cancer cell proliferation, tumor growth, or metastasis of an individual having, or at risk of having, a cancer associated with IRF4 comprises administering to the individual a compound comprising a IRF4 specific inhibitor, thereby reducing or inhibiting cancer cell proliferation, tumor growth, or metastasis in the individual. In certain embodiments, the individual has, or is at risk of having, blood cancer, myeloma, multiple myeloma (MM), B cell malignancies, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia. Examples of cancers associated with IRF4 treatable, preventable, and/or ameliorable with the methods provided herein include blood cancer, myeloma, multiple myeloma (MM), B cell malignancies, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia. In certain embodiments, the B-cell lymphoma is a non-Hodgkin's B-cell lymphoma. Examples of non-Hodgkin's B-cell lymphoma of certain embodiments that can be treated with compounds provided herein include, but are not limited to, diffuse large B cell lymphoma (DLBCL), activated B-cell lymphoma (ABC-DLBCL), germinal center B-cell lymphoma (GCB DLBCL), follicular lymphoma, mucosa-associated lymphatic tissue lymphoma (MALT), small cell lymphocytic lymphoma, chronic lymphocytic leukemia, mantle cell lymphoma (MCL), Burkitt lymphoma, mediastinal large B cell lymphoma, Waldenstrom macroglobulinemia, nodal marginal zone B cell lymphoma (NMZL), splenic marginal zone lymphoma (SMZL), intravascular large B-cell lymphoma, primary effusion lymphoma, and lymphomatoid granulomatosis. In certain embodiments, the T-cell lymphoma that can be treated with compounds provided herein include, but are not limited to, peripheral T-cell lymphoma, adult T cell leukemia/lymphoma (ATLL), and anaplastic large cell lymphoma (ALCL). In certain embodiments, the leukemia that can be treated with compounds provided herein includes, but is not limited to, acute lymphocytic leukemia (ALL). In certain embodiments, the compound comprises an antisense compound targeted to IRF4. In certain embodiments, the compound comprises an oligonucleotide targeted to IRF4. In certain embodiments, the compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 8 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a modified oligonucleotide 16 to 80 linked nucleosides in length and having a nucleobase sequence comprising the nucleobase sequence of any one of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a modified oligonucleotide consisting of the nucleobase sequence of any one of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a modified oligonucleotide of 16 to 80 linked nucleosides in length having a nucleobase sequence comprising any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303. In certain embodiments, the compound comprises a modified oligonucleotide having a nucleobase sequence consisting of any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303. In any of the foregoing embodiments, the modified oligonucleotide can be 10 to 30 linked nucleosides in length. In certain embodiments, the compound is ION 690890, 935658, 935696, 935762, 935918, 935968, 882800, 1012795, 1014095, and 1014834. In any of the foregoing embodiments, the compound can be single-stranded or double-stranded. In any of the foregoing embodiments, the compound can be an antisense compound or oligomeric compound. In certain embodiments, the compound is administered to the individual parenterally. In certain embodiments, the individual is identified as having or at risk of having a cancer associated with IRF4.
  • Certain embodiments are drawn to a compound comprising a IRF4 specific inhibitor for use in treating cancer. In certain embodiments, the cancer is a blood cancer, myeloma, multiple myeloma (MM), B cell malignancy, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia. In certain embodiments, the B-cell lymphoma is a non-Hodgkin's B-cell lymphoma. Examples of non-Hodgkin's B-cell lymphoma of certain embodiments that can be treated with compounds provided herein include, but are not limited to, diffuse large B cell lymphoma (DLBCL), activated B-cell lymphoma (ABC-DLBCL), germinal center B-cell lymphoma (GCB DLBCL), follicular lymphoma, mucosa-associated lymphatic tissue lymphoma (MALT), small cell lymphocytic lymphoma, chronic lymphocytic leukemia, mantle cell lymphoma (MCL), Burkitt lymphoma, mediastinal large B cell lymphoma, Waldenstrom macroglobulinemia, nodal marginal zone B cell lymphoma (NMZL), splenic marginal zone lymphoma (SMZL), intravascular large B-cell lymphoma, primary effusion lymphoma, and lymphomatoid granulomatosis. In certain embodiments, the T-cell lymphoma that can be treated with compounds provided herein include, but are not limited to, peripheral T-cell lymphoma, adult T cell leukemia/lymphoma (ATLL), and anaplastic large cell lymphoma (ALCL). In certain embodiments, the leukemia that can be treated with compounds provided herein includes, but is not limited to, acute lymphocytic leukemia (ALL). In certain embodiments, the compound comprises an antisense compound targeted to IRF4. In certain embodiments, the compound comprises an oligonucleotide targeted to IRF4. In certain embodiments, the compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 8 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a modified oligonucleotide 16 to 80 linked nucleosides in length and having a nucleobase sequence comprising the nucleobase sequence of any one of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a modified oligonucleotide consisting of the nucleobase sequence of any one of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a modified oligonucleotide of 16 to 80 linked nucleosides in length having a nucleobase sequence comprising any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303. In certain embodiments, the compound comprises a modified oligonucleotide having a nucleobase sequence consisting of any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303. In any of the foregoing embodiments, the modified oligonucleotide can be 10 to 30 linked nucleosides in length. In certain embodiments, the compound is ION 690890, 935658, 935696, 935762, 935918, 935968, 882800, 1012795, 1014095, and 1014834. In any of the foregoing embodiments, the compound can be single-stranded or double-stranded. In any of the foregoing embodiments, the compound can be an antisense compound or oligomeric compound.
  • Certain embodiments are drawn to a compound comprising a IRF4 specific inhibitor for use in reducing or inhibiting cancer cell proliferation, tumor growth, or metastasis in an individual having cancer. In certain embodiments, the cancer is a blood cancer, myeloma, multiple myeloma (MM), B cell malignancy, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia. In certain embodiments, the compound comprises an antisense compound targeted to IRF4. In certain embodiments, the compound comprises an oligonucleotide targeted to IRF4. In certain embodiments, the compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 8 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a modified oligonucleotide 16 to 80 linked nucleosides in length and having a nucleobase sequence comprising the nucleobase sequence of any one of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a modified oligonucleotide consisting of the nucleobase sequence of any one of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a modified oligonucleotide of 16 to 80 linked nucleosides in length having a nucleobase sequence comprising any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303. In certain embodiments, the compound comprises a modified oligonucleotide having a nucleobase sequence consisting of any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303. In any of the foregoing embodiments, the modified oligonucleotide can be 10 to 30 linked nucleosides in length. In certain embodiments, the compound is ION 690890, 935658, 935696, 935762, 935918, 935968, 882800, 1012795, 1014095, and 1014834. In any of the foregoing embodiments, the compound can be single-stranded or double-stranded. In any of the foregoing embodiments, the compound can be an antisense compound or oligomeric compound.
  • Certain embodiments are drawn to use of a compound comprising a IRF4 specific inhibitor for the manufacture or preparation of a medicament for treating cancer. Certain embodiments are drawn to use of a compound comprising a IRF4 specific inhibitor for the preparation of a medicament for treating a cancer associated with IRF4. In certain embodiments, the cancer is a blood cancer, myeloma, multiple myeloma (MM), B cell malignancy, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia. In certain embodiments, the B-cell lymphoma is a non-Hodgkin's B-cell lymphoma. Examples of non-Hodgkin's B-cell lymphoma of certain embodiments that can be treated with compounds provided herein include, but are not limited to, diffuse large B cell lymphoma (DLBCL), activated B-cell lymphoma (ABC-DLBCL), germinal center B-cell lymphoma (GCB DLBCL), follicular lymphoma, mucosa-associated lymphatic tissue lymphoma (MALT), small cell lymphocytic lymphoma, chronic lymphocytic leukemia, mantle cell lymphoma (MCL), Burkitt lymphoma, mediastinal large B cell lymphoma, Waldenström macroglobulinemia, nodal marginal zone B cell lymphoma (NMZL), splenic marginal zone lymphoma (SMZL), intravascular large B-cell lymphoma, primary effusion lymphoma, and lymphomatoid granulomatosis. In certain embodiments, the T-cell lymphoma that can be treated with compounds provided herein include, but are not limited to, peripheral T-cell lymphoma, adult T cell leukemia/lymphoma (ATLL), and anaplastic large cell lymphoma (ALCL). In certain embodiments, the leukemia that can be treated with compounds provided herein includes, but is not limited to, acute lymphocytic leukemia (ALL). In certain embodiments, the compound comprises an antisense compound targeted to IRF4. In certain embodiments, the compound comprises an oligonucleotide targeted to IRF4. In certain embodiments, the compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 8 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a modified oligonucleotide 16 to 80 linked nucleosides in length and having a nucleobase sequence comprising the nucleobase sequence of any one of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a modified oligonucleotide consisting of the nucleobase sequence of any one of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a modified oligonucleotide of 16 to 80 linked nucleosides in length having a nucleobase sequence comprising any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303. In certain embodiments, the compound comprises a modified oligonucleotide having a nucleobase sequence consisting of any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303. In any of the foregoing embodiments, the modified oligonucleotide can be 10 to 30 linked nucleosides in length. In certain embodiments, the compound is ION 690890, 935658, 935696, 935762, 935918, 935968, 882800, 1012795, 1014095, and 1014834. In any of the foregoing embodiments, the compound can be single-stranded or double-stranded. In any of the foregoing embodiments, the compound can be an antisense compound or oligomeric compound.
  • Certain embodiments are drawn to use of a compound comprising a IRF4 specific inhibitor for the manufacture or preparation of a medicament for reducing or inhibiting cancer cell proliferation, tumor growth, or metastasis in an individual having cancer. In certain embodiments, the cancer is a blood cancer, myeloma, multiple myeloma (MM), B cell malignancy, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia. Certain embodiments are drawn to use of a compound comprising a TRF4 specific inhibitor for the preparation of a medicament for reducing or inhibiting cancer cell proliferation, tumor growth, or metastasis in an individual having cancer. In certain embodiments, the cancer is a blood cancer, myeloma, multiple myeloma (MM), B cell malignancy, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia. In certain embodiments, the B-cell lymphoma is a non-Hodgkin's B-cell lymphoma. Examples of non-Hodgkin's B-cell lymphoma of certain embodiments include, but are not limited to, diffuse large B cell lymphoma (DLBCL), activated B-cell lymphoma (ABC-DLBCL), germinal center B-cell lymphoma (GCB DLBCL), follicular lymphoma, mucosa-associated lymphatic tissue lymphoma (MALT), small cell lymphocytic lymphoma, chronic lymphocytic leukemia, mantle cell lymphoma (MCL), Burkitt lymphoma, mediastinal large B cell lymphoma, Waldenström macroglobulinemia, nodal marginal zone B cell lymphoma (NMZL), splenic marginal zone lymphoma (SMZL), intravascular large B-cell lymphoma, primary effusion lymphoma, and lymphomatoid granulomatosis. In certain embodiments, the T-cell lymphoma includes, but is not limited to, peripheral T-cell lymphoma, adult T cell leukemia/lymphoma (ATLL), and anaplastic large cell lymphoma (ALCL). In certain embodiments, the leukemia includes, but is not limited to, acute lymphocytic leukemia (ALL). In certain embodiments, the compound comprises an antisense compound targeted to TRF4. In certain embodiments, the compound comprises an oligonucleotide targeted to IRF4. In certain embodiments, the compound comprises a modified oligonucleotide 8 to 80 linked nucleosides in length and having a nucleobase sequence comprising at least 8 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a modified oligonucleotide 16 to 80 linked nucleosides in length and having a nucleobase sequence comprising the nucleobase sequence of any one of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a modified oligonucleotide consisting of the nucleobase sequence of any one of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a modified oligonucleotide of 16 to 80 linked nucleosides in length having a nucleobase sequence comprising any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303. In certain embodiments, the compound comprises a modified oligonucleotide having a nucleobase sequence consisting of any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303. In any of the foregoing embodiments, the modified oligonucleotide can be 10 to 30 linked nucleosides in length. In certain embodiments, the compound is ION 690890, 935658, 935696, 935762, 935918, 935968, 882800, 1012795, 1014095, and 1014834. In any of the foregoing embodiments, the compound can be single-stranded or double-stranded. In any of the foregoing embodiments, the compound can be an antisense compound or oligomeric compound.
  • In any of the foregoing methods or uses, the compound can be targeted to IRF4. In certain embodiments, the compound comprises or consists of a modified oligonucleotide, for example a modified oligonucleotide 8 to 80 linked nucleosides in length, 10 to 30 linked nucleosides in length, 12 to 30 linked nucleosides in length, or 20 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is at least 80%, 85%, 90%, 95% or 100% complementary to any of the nucleobase sequences recited in SEQ ID NOs: 1-2. In certain embodiments, the modified oligonucleotide comprises at least one modified internucleoside linkage, at least one modified sugar and/or at least one modified nucleobase. In certain embodiments, the modified internucleoside linkage is a phosphorothioate internucleoside linkage, the modified sugar is a bicyclic sugar or a 2′-O-methoxyethyl, and the modified nucleobase is a 5-methylcytosine. In certain embodiments, the modified oligonucleotide comprises a gap segment consisting of linked deoxynucleosides; a 5′ wing segment consisting of linked nucleosides; and a 3′ wing segment consisting of linked nucleosides, wherein the gap segment is positioned immediately adjacent to and between the 5′ wing segment and the 3′ wing segment and wherein each nucleoside of each wing segment comprises a modified sugar.
  • In any of the foregoing embodiments, the modified oligonucleotide can be 12 to 30, 15 to 30, 15 to 25, 15 to 24, 16 to 24, 17 to 24, 18 to 24, 19 to 24, 20 to 24, 19 to 22, 20 to 22, 16 to 20, or 17 or 20 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is at least 80%, 85%, 90%, 95% or 100% complementary to any of the nucleobase sequences recited in SEQ ID NOs: 1-2. In certain embodiments, the modified oligonucleotide comprises at least one modified internucleoside linkage, at least one modified sugar and/or at least one modified nucleobase. In certain embodiments, the modified internucleoside linkage is a phosphorothioate internucleoside linkage, the modified sugar is a bicyclic sugar or a 2′-O-methoxyethyl, and the modified nucleobase is a 5-methylcytosine. In certain embodiments, the modified oligonucleotide comprises a gap segment consisting of linked 2′-deoxynucleosides; a 5′ wing segment consisting of linked nucleosides; and a 3′ wing segment consisting of linked nucleosides, wherein the gap segment is positioned immediately adjacent to and between the 5′ wing segment and the 3′ wing segment and wherein each nucleoside of each wing segment comprises a modified sugar.
  • In any of the foregoing methods or uses, the compound can comprise or consist of a modified oligonucleotide 16 to 80 linked nucleosides in length and having a nucleobase sequence comprising any one of SEQ ID NOs: 3-3383, wherein the modified oligonucleotide comprises:
      • a gap segment consisting of linked 2′-deoxynucleosides;
      • a 5′ wing segment consisting of linked nucleosides; and
      • a 3′ wing segment consisting of linked nucleosides;
  • wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment and wherein each nucleoside of each wing segment comprises a modified sugar. In certain embodiments, the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • In any of the foregoing methods or uses, the compound can comprise or consist of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in any one of SEQ ID NOs: 2021, 560, 559, 1330, 1540, or 3303, wherein the modified oligonucleotide comprises:
      • a gap segment consisting of linked deoxynucleosides;
      • a 5′ wing segment consisting of linked nucleosides; and
      • a 3′ wing segment consisting of linked nucleosides;
  • wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment and wherein each nucleoside of each wing segment comprises a modified sugar. In certain embodiments, the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • In any of the foregoing methods or uses, the compound can comprise or consist of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in any one of SEQ ID NOs: 1330 or 3303, wherein the modified oligonucleotide comprises:
  • a gap segment consisting of ten linked deoxynucleosides;
  • a 5′ wing segment consisting of three linked nucleosides; and
  • a 3′ wing segment consisting of three linked nucleosides;
  • wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of each wing segment comprises a cEt nucleoside; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine. In certain embodiments, the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • In any of the foregoing methods or uses, the compound can comprise or consist of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in any one of SEQ ID NOs: 559 or 560, wherein the modified oligonucleotide comprises:
  • a gap segment consisting of ten linked deoxynucleosides;
  • a 5′ wing segment consisting of one linked nucleoside; and
  • a 3′ wing segment consisting of five linked nucleosides;
  • wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein the 5′ wing segment comprises a cEt nucleoside; wherein the 3′ wing segment comprises a cEt nucleoside, a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, a 2′-O-methoxyethyl nucleoside, and a cEt nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine. In certain embodiments, the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • In any of the foregoing methods or uses, the compound can comprise or consist of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in any one of SEQ ID NOs: 1330 or 2021, wherein the modified oligonucleotide comprises:
  • a gap segment consisting of ten linked deoxynucleosides;
  • a 5′ wing segment consisting of two linked nucleosides; and
  • a 3′ wing segment consisting of four linked nucleosides;
  • wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of the 5′ wing segment comprises a cEt nucleoside; wherein the 3′ wing segment comprises a cEt nucleoside, a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, and a 2′-O-methoxyethyl nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine. In certain embodiments, the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • In any of the foregoing methods or uses, the compound can comprise or consist of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in SEQ ID NO: 560, wherein the modified oligonucleotide comprises:
  • a gap segment consisting of nine linked deoxynucleosides;
  • a 5′ wing segment consisting of two linked nucleosides; and
  • a 3′ wing segment consisting of five linked nucleosides;
  • wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of the 5′ wing segment comprises a cEt nucleoside; wherein the 3′ wing segment comprises a cEt nucleoside, a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, a 2′-O-methoxyethyl nucleoside, and a cEt nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine. In certain embodiments, the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • In any of the foregoing methods or uses, the compound can comprise or consist of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in SEQ ID NOs: 2021, wherein the modified oligonucleotide comprises:
  • a gap segment consisting of nine linked deoxynucleosides;
  • a 5′ wing segment consisting of two linked nucleosides; and
  • a 3′ wing segment consisting of five linked nucleosides;
  • wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of the 5′ wing segment comprises a cEt nucleoside; wherein the 3′ wing segment comprises a 2′-O-methoxyethyl nucleoside, a 2′-O-methoxyethyl nucleoside, a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, and a cEt nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine. In certain embodiments, the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • In any of the foregoing methods or uses, the compound can comprise or consist of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in SEQ ID NOs: 1540, wherein the modified oligonucleotide comprises:
  • a gap segment consisting of nine linked deoxynucleosides;
  • a 5′ wing segment consisting of two linked nucleosides; and
  • a 3′ wing segment consisting of five linked nucleosides;
  • wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of the 5′ wing segment comprises a cEt nucleoside; wherein the 3′ wing segment comprises a 2′-O-methoxyethyl nucleoside, a 2′-O-methoxyethyl nucleoside, a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, and a cEt nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine. In certain embodiments, the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • In any of the foregoing methods or uses, the compound can comprise or consist of a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in SEQ ID NOs: 560, wherein the modified oligonucleotide comprises:
  • a gap segment consisting of nine linked deoxynucleosides;
  • a 5′ wing segment consisting of two linked nucleosides; and
  • a 3′ wing segment consisting of five linked nucleosides;
  • wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of the 5′ wing segment comprises a cEt nucleoside; wherein the 3′ wing segment comprises a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, a 2′-O-methoxyethyl nucleoside, a cEt nucleoside, and a 2′-O-methoxyethyl nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine. In certain embodiments, the modified oligonucleotide is 16-30 linked nucleosides in length. In certain embodiments, the modified oligonucleotide is 16 linked nucleosides in length.
  • In any of the foregoing methods or uses, the compound can comprise or consist of ION 935918 or salt thereof, having the following chemical structure:
  • Figure US20220241320A1-20220804-C00005
  • In any of the foregoing methods or uses, the compound can comprise or consist of the sodium salt of ION 935918, having the following chemical structure:
  • Figure US20220241320A1-20220804-C00006
  • In any of the foregoing methods or uses, the compound can comprise or consist of ION 935968 or salt thereof, having the following chemical structure:
  • Figure US20220241320A1-20220804-C00007
  • In any of the foregoing methods or uses, the compound can comprise or consist of the sodium salt of ION 935968, having the following chemical structure:
  • Figure US20220241320A1-20220804-C00008
  • In any of the foregoing methods or uses, the compound can be administered parenterally. For example, in certain embodiments the compound can be administered through injection or infusion. Parenteral administration includes subcutaneous administration, intravenous administration, intramuscular administration, intraarterial administration, intraperitoneal administration, or intracranial administration, e.g. intrathecal or intracerebroventricular administration.
  • Certain Combinations and Combination Therapies
  • In certain embodiments, a first agent comprising a compound described herein is co-administered with one or more secondary agents. In certain embodiments, such second agents are designed to treat the same disease, disorder, or condition as the first agent described herein. In certain embodiments, such second agents are designed to treat a different disease, disorder, or condition as the first agent described herein. In certain embodiments, a first agent is designed to treat an undesired side effect of a second agent. In certain embodiments, second agents are co-administered with the first agent to treat an undesired effect of the first agent. In certain embodiments, such second agents are designed to treat an undesired side effect of one or more pharmaceutical compositions as described herein. In certain embodiments, second agents are co-administered with the first agent to produce a combinational effect. In certain embodiments, second agents are co-administered with the first agent to produce a synergistic effect. In certain embodiments, the co-administration of the first and second agents permits use of lower dosages than would be required to achieve a therapeutic or prophylactic effect if the agents were administered as independent therapy.
  • In certain embodiments, one or more compounds or compositions provided herein are co-administered with one or more secondary agents. In certain embodiments, one or more compounds or compositions provided herein and one or more secondary agents, are administered at different times. In certain embodiments, one or more compounds or compositions provided herein and one or more secondary agents, are prepared together in a single formulation. In certain embodiments, one or more compounds or compositions provided herein and one or more secondary agents, are prepared separately. In certain embodiments, a secondary agent is selected from: proteasome inhibitors including but not limited to bortezomib, carfilzomib, and ixazomib; BTK inhibitors including but not limited to ibrutinib; IMiDs including but not limited to thalidomide, lenalidomide, and pomalidomide; BCL2 inhibitors including but not limited to venetoclax; HDAC inhibitors including but not limited to panobinostat; CDK inhibitors including but not limited to dinaciclib; XPO1 inhibitors including but not limited to selinexor; BET inhibitors including but not limited to CPI-0610; anti-CD38 antibodies including but not limited to daratumumab, isatuximab, and MOR202; anti-CD319 or anti-SLAMF7 antibodies including but not limited to elotuzumab; dexamethasone, cisplatin, doxorubicin, cyclophosphamide, and etoposide.
  • Certain embodiments are directed to the use of a compound targeted to IRF4 as described herein in combination with a secondary agent. In particular embodiments such use is in a method of treating a patient suffering from cancer including, but not limited to, blood cancer, myeloma, multiple myeloma (MM), B cell malignancies, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia. In certain embodiments, such use is in the preparation or manufacture of a medicament for treating cancer including, but not limited to, blood cancer, myeloma, multiple myeloma (MM), B cell malignancies, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia. In certain embodiments, the B-cell lymphoma is a non-Hodgkin's B-cell lymphoma. Examples of non-Hodgkin's B-cell lymphoma of certain embodiments that can be treated with compounds provided herein include, but are not limited to, diffuse large B cell lymphoma (DLBCL), activated B-cell lymphoma (ABC-DLBCL), germinal center B-cell lymphoma (GCB DLBCL), follicular lymphoma, mucosa-associated lymphatic tissue lymphoma (MALT), small cell lymphocytic lymphoma, chronic lymphocytic leukemia, mantle cell lymphoma (MCL), Burkitt lymphoma, mediastinal large B cell lymphoma, Waldenström macroglobulinemia, nodal marginal zone B cell lymphoma (NMZL), splenic marginal zone lymphoma (SMZL), intravascular large B-cell lymphoma, primary effusion lymphoma, and lymphomatoid granulomatosis. In certain embodiments, the T-cell lymphoma includes, but is not limited to, peripheral T-cell lymphoma, adult T cell leukemia/lymphoma (ATLL), and anaplastic large cell lymphoma (ALCL). In certain embodiments, the leukemia includes, but is not limited to, acute lymphocytic leukemia (ALL). In certain embodiments, a secondary agent is selected from: proteasome inhibitors including but not limited to bortezomib, carfilzomib, and ixazomib; BTK inhibitors including but not limited to ibrutinib; IMiDs including but not limited to thalidomide, lenalidomide, and pomalidomide; BCL2 inhibitors including but not limited to venetoclax; HDAC inhibitors including but not limited to panobinostat; CDK inhibitors including but not limited to dinaciclib; XPO1 inhibitors including but not limited to selinexor; BET inhibitors including but not limited to CPI-0610; anti-CD38 antibodies including but not limited to daratumumab, isatuximab, and MOR202; anti-CD319 or anti-SLAMF7 antibodies including but not limited to elotuzumab; dexamethasone, cisplatin, doxorubicin, cyclophosphamide, and etoposide.
  • Certain embodiments are drawn to a combination of a compound targeted to IRF4 as described herein and a secondary agent, such as a secondary agent selected from: proteasome inhibitors including but not limited to bortezomib, carfilzomib, and ixazomib; BTK inhibitors including but not limited to ibrutinib; IMiDs including but not limited to thalidomide, lenalidomide, and pomalidomide; BCL2 inhibitors including but not limited to venetoclax; HDAC inhibitors including but not limited to panobinostat; CDK inhibitors including but not limited to dinaciclib; XPO1 inhibitors including but not limited to selinexor; BET inhibitors including but not limited to CPI-0610; dexamethasone, thalidomide, cisplatin, doxorubicin, cyclophosphamide, and etoposide. In certain embodiments, such a combination of a compound targeted to IRF4 as described herein and a secondary agent, such as a secondary agent selected from: proteasome inhibitors including but not limited to bortezomib, carfilzomib, and ixazomib; BTK inhibitors including but not limited to ibrutinib; IMiDs including but not limited to lenalidomide; BCL2 inhibitors including but not limited to venetoclax; HDAC inhibitors including but not limited to panobinostat; CDK inhibitors including but not limited to dinaciclib; XPO1 inhibitors including but not limited to selinexor; BET inhibitors including but not limited to CPI-0610; anti-CD38 antibodies including but not limited to daratumumab, isatuximab, and MOR202; anti-CD319 or anti-SLAMF7 antibodies including but not limited to elotuzumab; dexamethasone, cisplatin, doxorubicin, cyclophosphamide, and etoposide. Such combinations can be useful for reducing or inhibiting cancer cell proliferation, tumor growth, or metastasis and/or treating cancer including, but not limited to, blood cancer, mycloma, multiple mycloma (MM), B cell malignancies, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia.
  • In certain embodiments the compound targeted to IRF4 as described herein and the secondary agent are used in combination treatment by administering the two agents simultaneously, separately or sequentially. In certain embodiments the two agents are formulated as a fixed dose combination product. In other embodiments the two agents are provided to the patient as separate units which can then either be taken simultaneously or serially (sequentially).
  • Certain Compounds
  • In certain embodiments, compounds described herein can be antisense compounds. In certain embodiments, the antisense compound comprises or consists of an oligomeric compound. In certain embodiments, the oligomeric compound comprises a modified oligonucleotide. In certain embodiments, the modified oligonucleotide has a nucleobase sequence complementary to that of a target nucleic acid.
  • In certain embodiments, a compound described herein comprises or consists of a modified oligonucleotide. In certain embodiments, the modified oligonucleotide has a nucleobase sequence complementary to that of a target nucleic acid.
  • In certain embodiments, a compound or antisense compound is single-stranded. Such a single-stranded compound or antisense compound comprises or consists of an oligomeric compound. In certain embodiments, such an oligomeric compound comprises or consists of an oligonucleotide and optionally a conjugate group. In certain embodiments, the oligonucleotide is an antisense oligonucleotide. In certain embodiments, the oligonucleotide is modified. In certain embodiments, the oligonucleotide of a single-stranded antisense compound or oligomeric compound comprises a self-complementary nucleobase sequence.
  • In certain embodiments, compounds are double-stranded. Such double-stranded compounds comprise a first modified oligonucleotide having a region complementary to a target nucleic acid and a second modified oligonucleotide having a region complementary to the first modified oligonucleotide. In certain embodiments, the modified oligonucleotide is an RNA oligonucleotide. In such embodiments, the thymine nucleobase in the modified oligonucleotide is replaced by a uracil nucleobase. In certain embodiments, compound comprises a conjugate group. In certain embodiments, one of the modified oligonucleotides is conjugated. In certain embodiments, both the modified oligonucleotides are conjugated. In certain embodiments, the first modified oligonucleotide is conjugated. In certain embodiments, the second modified oligonucleotide is conjugated. In certain embodiments, the first modified oligonucleotide is 12-30 linked nucleosides in length and the second modified oligonucleotide is 12-30 linked nucleosides in length. In certain embodiments, one of the modified oligonucleotides has a nucleobase sequence comprising at least 8 contiguous nucleobases of any of SEQ ID NOs: 3-3383.
  • In certain embodiments, antisense compounds are double-stranded. Such double-stranded antisense compounds comprise a first oligomeric compound having a region complementary to a target nucleic acid and a second oligomeric compound having a region complementary to the first oligomeric compound. The first oligomeric compound of such double stranded antisense compounds typically comprises or consists of a modified oligonucleotide and optionally a conjugate group. The oligonucleotide of the second oligomeric compound of such double-stranded antisense compound may be modified or unmodified. Either or both oligomeric compounds of a double-stranded antisense compound may comprise a conjugate group. The oligomeric compounds of double-stranded antisense compounds may include non-complementary overhanging nucleosides.
  • Examples of single-stranded and double-stranded compounds include but are not limited to oligonucleotides, siRNAs, microRNA targeting oligonucleotides, and single-stranded RNAi compounds, such as small hairpin RNAs (shRNAs), single-stranded siRNAs (ssRNAs), and microRNA mimics.
  • In certain embodiments, a compound described herein has a nucleobase sequence that, when written in the 5′ to 3′ direction, comprises the reverse complement of the target segment of a target nucleic acid to which it is targeted.
  • In certain embodiments, a compound described herein comprises an oligonucleotide 10 to 30 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 12 to 30 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 12 to 22 linked subunits in length. In certain embodiments, compound described herein comprises an oligonucleotide 14 to 30 linked subunits in length. In certain embodiments, compound described herein comprises an oligonucleotide 14 to 20 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 15 to 30 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 15 to 20 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 16 to 30 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 16 to 20 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 17 to 30 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 17 to 20 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 18 to 30 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 18 to 21 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 18 to 20 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 20 to 30 linked subunits in length. In other words, such oligonucleotides are 12 to 30 linked subunits, 14 to 30 linked subunits, 14 to 20 subunits, 15 to 30 subunits, 15 to 20 subunits, 16 to 30 subunits, 16 to 20 subunits, 17 to 30 subunits, 17 to 20 subunits, 18 to 30 subunits, 18 to 20 subunits, 18 to 21 subunits, 20 to 30 subunits, or 12 to 22 linked subunits in length, respectively. In certain embodiments, a compound described herein comprises an oligonucleotide 14 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 16 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 17 linked subunits in length. In certain embodiments, compound described herein comprises an oligonucleotide 18 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 19 linked subunits in length. In certain embodiments, a compound described herein comprises an oligonucleotide 20 linked subunits in length. In other embodiments, a compound described herein comprises an oligonucleotide 8 to 80, 12 to 50, 13 to 30, 13 to 50, 14 to 30, 14 to 50, 15 to 30, 15 to 50, 16 to 30, 16 to 50, 17 to 30, 17 to 50, 18 to 22, 18 to 24, 18 to 30, 18 to 50, 19 to 22, 19 to 30, 19 to 50, or 20 to 30 linked subunits. In certain such embodiments, the compound described herein comprises an oligonucleotide 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, or 80 linked subunits in length, or a range defined by any two of the above values. In some embodiments the linked subunits are nucleotides, nucleosides, or nucleobases.
  • In certain embodiments, the compound may further comprise additional features or elements, such as a conjugate group, that are attached to the oligonucleotide. In certain embodiments, such compounds are antisense compounds. In certain embodiments, such compounds are oligomeric compounds. In embodiments where a conjugate group comprises a nucleoside (i.e. a nucleoside that links the conjugate group to the oligonucleotide), the nucleoside of the conjugate group is not counted in the length of the oligonucleotide.
  • In certain embodiments, compounds may be shortened or truncated. For example, a single subunit may be deleted from the 5′ end (5′ truncation), or alternatively from the 3′ end (3′ truncation). A shortened or truncated compound targeted to an IRF4 nucleic acid may have two subunits deleted from the 5′ end, or alternatively may have two subunits deleted from the 3′ end, of the compound. Alternatively, the deleted nucleosides may be dispersed throughout the compound.
  • When a single additional subunit is present in a lengthened compound, the additional subunit may be located at the 5′ or 3′ end of the compound. When two or more additional subunits are present, the added subunits may be adjacent to each other, for example, in a compound having two subunits added to the 5′ end (5′ addition), or alternatively to the 3′ end (3′ addition), of the compound. Alternatively, the added subunits may be dispersed throughout the compound.
  • It is possible to increase or decrease the length of a compound, such as an oligonucleotide, and/or introduce mismatch bases without eliminating activity (Woolf et al. Proc. Natl. Acad. Sci. USA 1992, 89:7305-7309; Gautschi et al. J. Natl. Cancer Inst. March 2001, 93:463-471; Maher and Dolnick Nuc. Acid. Res. 1998, 16:3341-3358). However, seemingly small changes in oligonucleotide sequence, chemistry and motif can make large differences in one or more of the many properties required for clinical development (Seth et al. J. Med. Chem. 2009, 52, 10; Egli et al. J. Am. Chem. Soc. 2011, 133, 16642).
  • In certain embodiments, compounds described herein are interfering RNA compounds (RNAi), which include double-stranded RNA compounds (also referred to as short-interfering RNA or siRNA) and single-stranded RNAi compounds (or ssRNA). Such compounds work at least in part through the RISC pathway to degrade and/or sequester a target nucleic acid (thus, include microRNA/microRNA-mimic compounds). As used herein, the term siRNA is meant to be equivalent to other terms used to describe nucleic acid molecules that are capable of mediating sequence specific RNAi, for example short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), short hairpin RNA (shRNA), short interfering oligonucleotide, short interfering nucleic acid, short interfering modified oligonucleotide, chemically modified siRNA, post-transcriptional gene silencing RNA (ptgsRNA), and others. In addition, as used herein, the term “RNAi” is meant to be equivalent to other terms used to describe sequence specific RNA interference, such as post transcriptional gene silencing, translational inhibition, or epigenetics.
  • In certain embodiments, a compound described herein can comprise any of the oligonucleotide sequences targeted to IRF4 described herein. In certain embodiments, the compound can be double-stranded. In certain embodiments, the compound comprises a first strand comprising at least an 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 contiguous nucleobase portion of any one of SEQ ID NOs: 3-3383 and a second strand. In certain embodiments, the compound comprises a first strand comprising the nucleobase sequence of any one of SEQ ID NOs: 3-3383 and a second strand. In certain embodiments, the compound comprises ribonucleotides in which the first strand has uracil (U) in place of thymine (T) in any one of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises (i) a first strand comprising a nucleobase sequence complementary to the site on IRF4 to which any of SEQ ID NOs: 3-3383 is targeted, and (ii) a second strand. In certain embodiments, the compound comprises one or more modified nucleotides in which the 2′ position in the sugar contains a halogen (such as fluorine group; 2′-F) or contains an alkoxy group (such as a methoxy group; 2′-OMe). In certain embodiments, the compound comprises at least one 2′-F sugar modification and at least one 2′-OMe sugar modification. In certain embodiments, the at least one 2′-F sugar modification and at least one 2′-OMe sugar modification are arranged in an alternating pattern for at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 contiguous nucleobases along a strand of the dsRNA compound. In certain embodiments, the compound comprises one or more linkages between adjacent nucleotides other than a naturally-occurring phosphodiester linkage Examples of such linkages include phosphoramide, phosphorothioate, and phosphorodithioate linkages. The compounds may also be chemically modified nucleic acid molecules as taught in U.S. Pat. No. 6,673,661. In other embodiments, the compound contains one or two capped strands, as disclosed, for example, by WO 00/63364, filed Apr. 19, 2000.
  • In certain embodiments, the first strand of the compound is an siRNA guide strand and the second strand of the compound is an siRNA passenger strand. In certain embodiments, the second strand of the compound is complementary to the first strand. In certain embodiments, each strand of the compound is 16, 17, 18, 19, 20, 21, 22, or 23 linked nucleosides in length. In certain embodiments, the first or second strand of the compound can comprise a conjugate group.
  • In certain embodiments, a compound described herein can comprise any of the oligonucleotide sequences targeted to IRF4 described herein. In certain embodiments, the compound is single stranded. In certain embodiments, such a compound is a single-stranded RNAi (ssRNAi) compound. In certain embodiments, the compound comprises at least an 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 contiguous nucleobase portion of any one of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises the nucleobase sequence of any one of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises ribonucleotides in which uracil (U) is in place of thymine (T) in any one of SEQ ID NOs: 3-3383. In certain embodiments, the compound comprises a nucleobase sequence complementary to the site on IRF4 to which any of SEQ ID NOs: 3-3383 is targeted. In certain embodiments, the compound comprises one or more modified nucleotides in which the 2′ position in the sugar contains a halogen (such as fluorine group; 2′-F) or contains an alkoxy group (such as a methoxy group; 2′-OMe). In certain embodiments, the compound comprises at least one 2′-F sugar modification and at least one 2′-OMe sugar modification. In certain embodiments, the at least one 2′-F sugar modification and at least one 2′-OMe sugar modification are arranged in an alternating pattern for at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 contiguous nucleobases along a strand of the compound. In certain embodiments, the compound comprises one or more linkages between adjacent nucleotides other than a naturally-occurring phosphodiester linkage. Examples of such linkages include phosphoramide, phosphorothioate, and phosphorodithioate linkages. The compounds may also be chemically modified nucleic acid molecules as taught in U.S. Pat. No. 6,673,661. In other embodiments, the compound contains a capped strand, as disclosed, for example, by WO 00/63364, filed Apr. 19, 2000. In certain embodiments, the compound consists of 16, 17, 18, 19, 20, 21, 22, or 23 linked nucleosides. In certain embodiments, the compound can comprise a conjugate group.
  • In certain embodiments, compounds described herein comprise modified oligonucleotides. Certain modified oligonucleotides have one or more asymmetric center and thus give rise to enantiomers, diastereomers, and other stereoisomeric configurations that may be defined, in terms of absolute stereochemistry, as (R) or (S), as α or β such as for sugar anomers, or as (D) or (L) such as for amino acids etc. Included in the modified oligonucleotides provided herein are all such possible isomers, including their racemic and optically pure forms, unless specified otherwise. Likewise, all cis- and trans-isomers and tautomeric forms are also included.
  • The compounds described herein include variations in which one or more atoms are replaced with a non-radioactive isotope or radioactive isotope of the indicated element. For example, compounds herein that comprise hydrogen atoms encompass all possible deuterium substitutions for each of the 1H hydrogen atoms. Isotopic substitutions encompassed by the compounds herein include but are not limited to: 2H or 3H in place of 1H, 13C or 14C in place of 12C, 15N in place of 14N, 17O or 18O in place of 16O, and 33S, 34S, 35S, or 36S in place of 32S. In certain embodiments, non-radioactive isotopic substitutions may impart new properties on the compound that are beneficial for use as a therapeutic or research tool. In certain embodiments, radioactive isotopic substitutions may make the compound suitable for research or diagnostic purposes, such as an imaging assay.
  • Certain Mechanisms
  • In certain embodiments, compounds described herein comprise or consist of modified oligonucleotides. In certain embodiments, compounds described herein are antisense compounds. In certain embodiments, compounds comprise oligomeric compounds. In certain embodiments, compounds described herein are capable of hybridizing to a target nucleic acid, resulting in at least one antisense activity. In certain embodiments, compounds described herein selectively affect one or more target nucleic acid. Such compounds comprise a nucleobase sequence that hybridizes to one or more target nucleic acid, resulting in one or more desired antisense activity and does not hybridize to one or more non-target nucleic acid or does not hybridize to one or more non-target nucleic acid in such a way that results in a significant undesired antisense activity.
  • In certain antisense activities, hybridization of a compound described herein to a target nucleic acid results in recruitment of a protein that cleaves the target nucleic acid. For example, certain compounds described herein result in RNase H mediated cleavage of the target nucleic acid. RNase H is a cellular endonuclease that cleaves the RNA strand of an RNA:DNA duplex. The DNA in such an RNA:DNA duplex need not be unmodified DNA. In certain embodiments, compounds described herein are sufficiently “DNA-like” to elicit RNase H activity. Further, in certain embodiments, one or more non-DNA-like nucleoside in the gap of a gapmer is tolerated.
  • In certain antisense activities, compounds described herein or a portion of the compound is loaded into an RNA-induced silencing complex (RISC), ultimately resulting in cleavage of the target nucleic acid. For example, certain compounds described herein result in cleavage of the target nucleic acid by Argonaute. Compounds that are loaded into RISC are RNAi compounds. RNAi compounds may be double-stranded (siRNA) or single-stranded (ssRNA).
  • In certain embodiments, hybridization of compounds described herein to a target nucleic acid does not result in recruitment of a protein that cleaves that target nucleic acid. In certain such embodiments, hybridization of the compound to the target nucleic acid results in alteration of splicing of the target nucleic acid. In certain embodiments, hybridization of the compound to a target nucleic acid results in inhibition of a binding interaction between the target nucleic acid and a protein or other nucleic acid. In certain such embodiments, hybridization of the compound to a target nucleic acid results in alteration of translation of the target nucleic acid.
  • Antisense activities may be observed directly or indirectly. In certain embodiments, observation or detection of an antisense activity involves observation or detection of a change in an amount of a target nucleic acid or protein encoded by such target nucleic acid, a change in the ratio of splice variants of a nucleic acid or protein, and/or a phenotypic change in a cell or animal.
  • Target Nucleic Acids, Target Regions and Nucleotide Sequences
  • In certain embodiments, compounds described herein comprise or consist of an oligonucleotide comprising a region that is complementary to a target nucleic acid. In certain embodiments, the target nucleic acid is an endogenous RNA molecule. In certain embodiments, the target nucleic acid encodes a protein. In certain such embodiments, the target nucleic acid is selected from: an mRNA and a pre-mRNA, including intronic, exonic and untranslated regions. In certain embodiments, the target RNA is an mRNA. In certain embodiments, the target nucleic acid is a pre-mRNA. In certain such embodiments, the target region is entirely within an intron. In certain embodiments, the target region spans an intron/exon junction. In certain embodiments, the target region is at least 50% within an intron.
  • Nucleotide sequences that encode IRF4 include, without limitation, the following: RefSEQ No. NM_002460.3 and NT_034880.3_TRUNC_328000_354000.
  • Hybridization
  • In some embodiments, hybridization occurs between a compound disclosed herein and a IRF4 nucleic acid. The most common mechanism of hybridization involves hydrogen bonding (e.g., Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding) between complementary nucleobases of the nucleic acid molecules.
  • Hybridization can occur under varying conditions. Hybridization conditions are sequence-dependent and are determined by the nature and composition of the nucleic acid molecules to be hybridized.
  • Methods of determining whether a sequence is specifically hybridizable to a target nucleic acid are well known in the art. In certain embodiments, the compounds provided herein are specifically hybridizable with a IRF4 nucleic acid.
  • Complementarily
  • An oligonucleotide is said to be complementary to another nucleic acid when the nucleobase sequence of such oligonucleotide or one or more regions thereof matches the nucleobase sequence of another oligonucleotide or nucleic acid or one or more regions thereof when the two nucleobase sequences are aligned in opposing directions. Nucleobase matches or complementary nucleobases, as described herein, are limited to the following pairs: adenine (A) and thymine (T), adenine (A) and uracil (U), cytosine (C) and guanine (G), and 5-methyl cytosine (mC) and guanine (G) unless otherwise specified. Complementary oligonucleotides and/or nucleic acids need not have nucleobase complementarity at each nucleoside and may include one or more nucleobase mismatches. An oligonucleotide is fully complementary or 100% complementary when such oligonucleotides have nucleobase matches at each nucleoside without any nucleobase mismatches.
  • In certain embodiments, compounds described herein comprise or consist of modified oligonucleotides. In certain embodiments, compounds described herein are antisense compounds. In certain embodiments, compounds comprise oligomeric compounds. Non-complementary nucleobases between a compound and a IRF4 nucleic acid may be tolerated provided that the compound remains able to specifically hybridize to a target nucleic acid. Moreover, a compound may hybridize over one or more segments of a IRF4 nucleic acid such that intervening or adjacent segments are not involved in the hybridization event (e.g., a loop structure, mismatch or hairpin structure).
  • In certain embodiments, the compounds provided herein, or a specified portion thereof, are, are at least, or are up to 70%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% complementary to a IRF4 nucleic acid, a target region, target segment, or specified portion thereof. In certain embodiments, the compounds provided herein, or a specified portion thereof, are 70% to 75%, 75% to 80%, 80% to 85%, 85% to 90%, 90% to 95%, 95% to 100%, or any number in between these ranges, complementary to a IRF4 nucleic acid, a target region, target segment, or specified portion thereof. Percent complementarity of a compound with a target nucleic acid can be determined using routine methods.
  • For example, a compound in which 18 of 20 nucleobases of the compound are complementary to a target region, and would therefore specifically hybridize, would represent 90 percent complementarity. In this example, the remaining non-complementary nucleobases may be clustered or interspersed with complementary nucleobases and need not be contiguous to each other or to complementary nucleobases. As such, a compound which is 18 nucleobases in length having four non-complementary nucleobases which are flanked by two regions of complete complementarity with the target nucleic acid would have 77.8% overall complementarity with the target nucleic acid. Percent complementarity of a compound with a region of a target nucleic acid can be determined routinely using BLAST programs (basic local alignment search tools) and PowerBLAST programs known in the art (Altschul et al., J. Mol. Biol., 1990, 215, 403 410; Zhang and Madden, Genome Res., 1997, 7, 649 656). Percent homology, sequence identity or complementarity, can be determined by, for example, the Gap program (Wisconsin Sequence Analysis Package, Version 8 for Unix, Genetics Computer Group, University Research Park, Madison Wis.), using default settings, which uses the algorithm of Smith and Waterman (Adv. Appl. Math., 1981, 2, 482 489).
  • In certain embodiments, compounds described herein, or specified portions thereof, are fully complementary (i.e. 100% complementary) to a target nucleic acid, or specified portion thereof. For example, a compound may be fully complementary to a IRF4 nucleic acid, or a target region, or a target segment or target sequence thereof. As used herein, “fully complementary” means each nucleobase of a compound is complementary to the corresponding nucleobase of a target nucleic acid. For example, a 20 nucleobase compound is fully complementary to a target sequence that is 400 nucleobases long, so long as there is a corresponding 20 nucleobase portion of the target nucleic acid that is fully complementary to the compound. Fully complementary can also be used in reference to a specified portion of the first and/or the second nucleic acid. For example, a 20 nucleobase portion of a 30 nucleobase compound can be “fully complementary” to a target sequence that is 400 nucleobases long. The 20 nucleobase portion of the 30 nucleobase compound is fully complementary to the target sequence if the target sequence has a corresponding 20 nucleobase portion wherein each nucleobase is complementary to the 20 nucleobase portion of the compound. At the same time, the entire 30 nucleobase compound may or may not be fully complementary to the target sequence, depending on whether the remaining 10 nucleobases of the compound are also complementary to the target sequence.
  • In certain embodiments, compounds described herein comprise one or more mismatched nucleobases relative to the target nucleic acid. In certain such embodiments, antisense activity against the target is reduced by such mismatch, but activity against a non-target is reduced by a greater amount. Thus, in certain such embodiments selectivity of the compound is improved. In certain embodiments, the mismatch is specifically positioned within an oligonucleotide having a gapmer motif. In certain such embodiments, the mismatch is at position 1, 2, 3, 4, 5, 6, 7, or 8 from the 5′-end of the gap region. In certain such embodiments, the mismatch is at position 9, 8, 7, 6, 5, 4, 3, 2, 1 from the 3′-end of the gap region. In certain such embodiments, the mismatch is at position 1, 2, 3, or 4 from the 5′-end of the wing region. In certain such embodiments, the mismatch is at position 4, 3, 2, or 1 from the 3′-end of the wing region. In certain embodiments, the mismatch is specifically positioned within an oligonucleotide not having a gapmer motif. In certain such embodiments, the mismatch is at position 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 from the 5′-end of the oligonucleotide. In certain such embodiments, the mismatch is at position, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 from the 3′-end of the oligonucleotide.
  • The location of a non-complementary nucleobase may be at the 5′ end or 3′ end of the compound. Alternatively, the non-complementary nucleobase or nucleobases may be at an internal position of the compound. When two or more non-complementary nucleobases are present, they may be contiguous (i.e. linked) or non-contiguous. In one embodiment, a non-complementary nucleobase is located in the wing segment of a gapmer oligonucleotide.
  • In certain embodiments, compounds described herein that are, or are up to 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleobases in length comprise no more than 4, no more than 3, no more than 2, or no more than 1 non-complementary nucleobase(s) relative to a target nucleic acid, such as a IRF4 nucleic acid, or specified portion thereof.
  • In certain embodiments, compounds described herein that are, or are up to 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleobases in length comprise no more than 6, no more than 5, no more than 4, no more than 3, no more than 2, or no more than 1 non-complementary nucleobase(s) relative to a target nucleic acid, such as a IRF4 nucleic acid, or specified portion thereof.
  • In certain embodiments, compounds described herein also include those which are complementary to a portion of a target nucleic acid. As used herein, “portion” refers to a defined number of contiguous (i.e. linked) nucleobases within a region or segment of a target nucleic acid. A “portion” can also refer to a defined number of contiguous nucleobases of a compound. In certain embodiments, the—compounds, are complementary to at least an 8 nucleobase portion of a target segment. In certain embodiments, the compounds are complementary to at least a 9 nucleobase portion of a target segment. In certain embodiments, the compounds are complementary to at least a 10 nucleobase portion of a target segment. In certain embodiments, the compounds are complementary to at least an 11 nucleobase portion of a target segment. In certain embodiments, the compounds are complementary to at least a 12 nucleobase portion of a target segment. In certain embodiments, the compounds are complementary to at least a 13 nucleobase portion of a target segment. In certain embodiments, the compounds are complementary to at least a 14 nucleobase portion of a target segment. In certain embodiments, the compounds are complementary to at least a 15 nucleobase portion of a target segment. In certain embodiments, the compounds are complementary to at least a 16 nucleobase portion of a target segment. Also contemplated are compounds that are complementary to at least a 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more nucleobase portion of a target segment, or a range defined by any two of these values.
  • Identity
  • The compounds provided herein may also have a defined percent identity to a particular nucleotide sequence, SEQ ID NO, or compound represented by a specific ION number, or portion thereof. In certain embodiments, compounds described herein are antisense compounds or oligomeric compounds. In certain embodiments, compounds described herein are modified oligonucleotides. As used herein, a compound is identical to the sequence disclosed herein if it has the same nucleobase pairing ability. For example, a RNA which contains uracil in place of thymidine in a disclosed DNA sequence would be considered identical to the DNA sequence since both uracil and thymidine pair with adenine. Shortened and lengthened versions of the compounds described herein as well as compounds having non-identical bases relative to the compounds provided herein also are contemplated. The non-identical bases may be adjacent to each other or dispersed throughout the compound. Percent identity of an compound is calculated according to the number of bases that have identical base pairing relative to the sequence to which it is being compared.
  • In certain embodiments, compounds described herein, or portions thereof, are, or are at least, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to one or more of the compounds or SEQ ID NOs, or a portion thereof, disclosed herein. In certain embodiments, compounds described herein are about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, or any percentage between such values, to a particular nucleotide sequence, SEQ ID NO, or compound represented by a specific ION number, or portion thereof, in which the compounds comprise an oligonucleotide having one or more mismatched nucleobases. In certain such embodiments, the mismatch is at position 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 from the 5′-end of the oligonucleotide. In certain such embodiments, the mismatch is at position, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 from the 3′-end of the oligonucleotide.
  • In certain embodiments, compounds described herein comprise or consist of antisense compounds. In certain embodiments, a portion of the antisense compound is compared to an equal length portion of the target nucleic acid. In certain embodiments, an 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleobase portion is compared to an equal length portion of the target nucleic acid.
  • In certain embodiments, compounds described herein comprise or consist of oligonucleotides. In certain embodiments, a portion of the oligonucleotide is compared to an equal length portion of the target nucleic acid. In certain embodiments, an 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleobase portion is compared to an equal length portion of the target nucleic acid.
  • Certain Modified Compounds
  • In certain embodiments, compounds described herein comprise or consist of oligonucleotides consisting of linked nucleosides. Oligonucleotides may be unmodified oligonucleotides (RNA or DNA) or may be modified oligonucleotides. Modified oligonucleotides comprise at least one modification relative to unmodified RNA or DNA (i.e., comprise at least one modified nucleoside (comprising a modified sugar moiety and/or a modified nucleobase) and/or at least one modified internucleoside linkage).
  • A. Modified Nucleosides
  • Modified nucleosides comprise a modified sugar moiety or a modified nucleobase or both a modified sugar moiety and a modified nucleobase.
  • 1. Modified Sugar Moieties
  • In certain embodiments, sugar moieties are non-bicyclic modified sugar moieties. In certain embodiments, modified sugar moieties are bicyclic or tricyclic sugar moieties. In certain embodiments, modified sugar moieties are sugar surrogates. Such sugar surrogates may comprise one or more substitutions corresponding to those of other types of modified sugar moieties.
  • In certain embodiments, modified sugar moieties are non-bicyclic modified sugar moieties comprising a furanosyl ring with one or more acyclic substituent, including but not limited to substituents at the 2′, 4′, and/or 5′ positions. In certain embodiments one or more acyclic substituent of non-bicyclic modified sugar moieties is branched. Examples of 2′-substituent groups suitable for non-bicyclic modified sugar moieties include but are not limited to: 2′-F, 2′-OCH3 (“OMe” or “O-methyl”), and 2′-O(CH2)2OCH3 (“MOE”). In certain embodiments, 2′-substituent groups are selected from among: halo, allyl, amino, azido, SH, CN, OCN, CF3, OCF3, O—C1-C10 alkoxy, O—C1-C10 substituted alkoxy, O—C1-C10 alkyl, O—C1-C10 substituted alkyl, S-alkyl, N(Rm)-alkyl, O-alkenyl, S-alkenyl, N(Rm)-alkenyl, O-alkynyl, S-alkynyl, N(Rm)-alkynyl, O-alkylenyl-O-alkyl, alkynyl, alkaryl, aralkyl, O-alkaryl, O-aralkyl, O(CH2)2SCH3, O(CH2)2O N(Rm)(Rn) or OCH2C(═O)—N(Rm)(Rm), where each Rm and Rn is, independently, H, an amino protecting group, or substituted or unsubstituted alkyl, and the 2′-substituent groups described in Cook et al., U.S. Pat. No. 6,531,584; Cook et al., U.S. Pat. No. 5,859,221; and Cook et al., U.S. Pat. No. 6,005,087. Certain embodiments of these 2′-substituent groups can be further substituted with one or more substituent groups independently selected from among: hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro (NO2), thiol, thioalkoxy, thioalkyl, halogen, alkyl, aryl, alkenyl and alkynyl. Examples of 4′-substituent groups suitable for linearly non-bicyclic modified sugar moieties include but are not limited to alkoxy (e.g., methoxy), alkyl, and those described in Manoharan et al., WO 2015/106128. Examples of 5′-substituent groups suitable for non-bicyclic modified sugar moieties include but are not limited to: 5′-methyl (R or S), 5′-vinyl, and 5′-methoxy. In certain embodiments, non-bicyclic modified sugars comprise more than one non-bridging sugar substituent, for example, 2′-F-5′-methyl sugar moieties and the modified sugar moieties and modified nucleosides described in Migawa et al., US2010/190837 and Rajeev et al., US2013/0203836.
  • In certain embodiments, a 2′-substituted nucleoside or 2′-non-bicyclic modified nucleoside comprises a sugar moiety comprising a linear 2′-substituent group selected from: F, NH2, N3, OCF3, OCH3, O(CH2)3NH2, CH2CH═CH2, OCH2CH═CH2, OCH2CH2OCH3, O(CH2)2SCH3, O(CH2)2ON(Rm)(Rn), O(CH2)2O(CH2)2N(CH3)2, and N-substituted acetamide (OCH2C(═O)—N(Rm)(Rn)), where each Rm and Rn is, independently, H, an amino protecting group, or substituted or unsubstituted C1-C10 alkyl.
  • In certain embodiments, a 2′-substituted nucleoside or 2′-non-bicyclic modified nucleoside comprises a sugar moiety comprising a linear 2′-substituent group selected from: F, OCF3, OCH3, OCH2CH2OCH3, O(CH2)2SCH3, O(CH2)2ON(CH3)2, O(CH2)2O(CH2)2N(CH3)2, and OCH2C(═O)—N(H)CH3 (“NMA”).
  • In certain embodiments, a 2′-substituted nucleoside or 2′-non-bicyclic modified nucleoside comprises a sugar moiety comprising a linear 2′-substituent group selected from: F, OCH3, and OCH2CH2OCH3.
  • Nucleosides comprising modified sugar moieties, such as non-bicyclic modified sugar moieties, are referred to by the position(s) of the substitution(s) on the sugar moiety of the nucleoside. For example, nucleosides comprising 2′-substituted or 2-modified sugar moieties are referred to as 2′-substituted nucleosides or 2-modified nucleosides.
  • Certain modified sugar moieties comprise a bridging sugar substituent that forms a second ring resulting in a bicyclic sugar moiety. In certain such embodiments, the bicyclic sugar moiety comprises a bridge between the 4′ and the 2′ furanose ring atoms. Examples of such 4′ to 2′ bridging sugar substituents include but are not limited to: 4′-CH2-2′, 4′-(CH2)2-2′, 4′-(CH2)3-2′, (“LNA”), 4′-CH2—S-2′, 4′-(CH2)2—O-2′ (“ENA”), 4′-CH(CH3)—O-2′ (referred to as “constrained ethyl” or “cEt” when in the S configuration), 4′-CH2—O—CH2-2′, 4′-CH2—N(R)-2′, 4′-CH(CH2OCH3)—O-2′ (“constrained MOE” or “cMOE”) and analogs thereof (see, e.g., Seth et al., U.S. Pat. No. 7,399,845, Bhat et al., U.S. Pat. No. 7,569,686, Swayze et al., U.S. Pat. No. 7,741,457, and Swayze et al., U.S. Pat. No. 8,022,193), 4′-C(CH3)(CH3)—O-2′ and analogs thereof (see, e.g., Seth et al., U.S. Pat. No. 8,278,283), 4′-CH2—N(OCH3)-2′ and analogs thereof (see, e.g., Prakash et al., U.S. Pat. No. 8,278,425), 4′-CH2—O—N(CH3)-2′ (see, e.g., Allerson et al., U.S. Pat. No. 7,696,345 and Allerson et al., U.S. Pat. No. 8,124,745), 4′-CH2—C(H)(CH3)-2′ (see, e.g., Zhou, et al., J. Org. Chem., 2009, 74, 118-134), 4′-CH2—C(═CH2)-2′ and analogs thereof (see e.g., Seth et al., U.S. Pat. No. 8,278,426), 4′-C(RaRb)—N(R)—O-2′, 4′-C(RaRb)—O—N(R)-2′, 4′-CH2—O—N(R)-2′, and 4′-CH2—N(R)—O-2′, wherein each R, Ra, and Rb is, independently, H, a protecting group, or C1-C12 alkyl (see, e.g. Imanishi et al., U.S. Pat. No. 7,427,672).
  • In certain embodiments, such 4′ to 2′ bridges independently comprise from 1 to 4 linked groups independently selected from: —┌C(Ra)(Rb)┐n—, —┌C(Ra)(Rb)┐n—O—, —C(Ra)═C(Rb)—, —C(Ra)═N—, —C(═NRa)—, —C(═O)—, —C(═S)—, —O—, —Si(Ra)2—, —S(═O)x—, and —N(Ra)—;
  • wherein:
  • x is 0, 1, or 2;
  • n is 1, 2, 3, or 4;
  • each Ra and Rb is, independently, H, a protecting group, hydroxyl, C1-C12 alkyl, substituted C1-C12 alkyl, C2-C12 alkenyl, substituted C2-C12 alkenyl, C2-C12 alkynyl, substituted C2-C12 alkynyl, C5-C20 aryl, substituted C5-C20 aryl, heterocycle radical, substituted heterocycle radical, heteroaryl, substituted heteroaryl, C5-C7 alicyclic radical, substituted C5-C7 alicyclic radical, halogen, OJ1, NJ1J2, SJ1, N3, COOJ1, acyl (C(═O)—H), substituted acyl, CN, sulfonyl (S(═O)2-J1), or sulfoxyl (S(═O)-J1); and each J1 and J2 is, independently, H, C1-C12 alkyl, substituted C1-C12 alkyl, C2-C12 alkenyl, substituted C2-C12 alkenyl, C2-C12 alkynyl, substituted C2-C12 alkynyl, C5-C20 aryl, substituted C5-C20 aryl, acyl (C(═O)—H), substituted acyl, a heterocycle radical, a substituted heterocycle radical, C1-C12 aminoalkyl, substituted C1-C12 aminoalkyl, or a protecting group.
  • Additional bicyclic sugar moieties are known in the art, see, for example: Freier et al., Nucleic Acids Research, 1997, 25(22), 4429-4443, Albaek et al., J. Org. Chem., 2006, 71, 7731-7740, Singh et al., Chem. Commun., 1998, 4, 455-456; Koshkin et al., Tetrahedron, 1998, 54, 3607-3630; Wahlestedt et al., Proc. Natl. Acad. Sci. U.S.A., 2000, 97, 5633-5638; Kumar et al., Bioorg. Med. Chem. Lett., 1998, 8, 2219-2222; Singh et al., J. Org. Chem., 1998, 63, 10035-10039; Srivastava et al., J Am. Chem. Soc., 2007, 129, 8362-8379; Elayadi et al., Curr. Opinion Invens. Drugs, 2001, 2, 558-561; Braasch et al., Chem. Biol., 2001, 8, 1-7; Orum et al., Curr. Opinion Mol. Ther., 2001, 3, 239-243; Wengel et al., U.S. Pat. No. 7,053,207, Imanishi et al., U.S. Pat. No. 6,268,490, Imanishi et al. U.S. Pat. No. 6,770,748, Imanishi et al., U.S. RE44,779; Wengel et al., U.S. Pat. No. 6,794,499, Wengel et al., U.S. Pat. No. 6,670,461; Wengel et al., U.S. Pat. No. 7,034,133, Wengel et al., U.S. Pat. No. 8,080,644; Wengel et al., U.S. Pat. No. 8,034,909; Wengel et al., U.S. Pat. No. 8,153,365; Wengel et al., U.S. Pat. No. 7,572,582; and Ramasamy et al., U.S. Pat. No. 6,525,191, Torsten et al., WO 2004/106356, Wengel et al., WO 1999/014226; Seth et al., WO 2007/134181; Seth et al., U.S. Pat. No. 7,547,684; Seth et al., U.S. Pat. No. 7,666,854; Seth et al., U.S. Pat. No. 8,088,746; Seth et al., U.S. Pat. No. 7,750,131; Seth et al., U.S. Pat. No. 8,030,467; Seth et al., U.S. Pat. No. 8,268,980; Seth et al., U.S. Pat. No. 8,546,556; Seth et al., U.S. Pat. No. 8,530,640; Migawa et al., U.S. Pat. No. 9,012,421; Seth et al., U.S. Pat. No. 8,501,805; Allerson et al., US2008/0039618; and Migawa et al., US2015/0191727.
  • In certain embodiments, bicyclic sugar moieties and nucleosides incorporating such bicyclic sugar moieties are further defined by isomeric configuration. For example, an LNA nucleoside (described herein) may be in the α-L configuration or in the β-D configuration.
  • Figure US20220241320A1-20220804-C00009
  • α-L-methyleneoxy (4′-CH2—O-2′) or α-L-LNA bicyclic nucleosides have been incorporated into oligonucleotides that showed antisense activity (Frieden et al., Nucleic Acids Research, 2003, 21, 6365-6372). Herein, general descriptions of bicyclic nucleosides include both isomeric configurations. When the positions of specific bicyclic nucleosides (e.g., LNA or cEt) are identified in exemplified embodiments herein, they are in the β-D configuration, unless otherwise specified.
  • In certain embodiments, modified sugar moieties comprise one or more non-bridging sugar substituent and one or more bridging sugar substituent (e.g., 5′-substituted and 4′-2′ bridged sugars).
  • In certain embodiments, modified sugar moieties are sugar surrogates. In certain such embodiments, the oxygen atom of the sugar moiety is replaced, e.g., with a sulfur, carbon or nitrogen atom. In certain such embodiments, such modified sugar moieties also comprise bridging and/or non-bridging substituents as described herein. For example, certain sugar surrogates comprise a 4′-sulfur atom and a substitution at the 2′-position (see, e.g., Bhat et al., U.S. Pat. No. 7,875,733 and Bhat et al., U.S. Pat. No. 7,939,677) and/or the 5′ position.
  • In certain embodiments, sugar surrogates comprise rings having other than 5 atoms. For example, in certain embodiments, a sugar surrogate comprises a six-membered tetrahydropyran (“THP”). Such tetrahydropyrans may be further modified or substituted. Nucleosides comprising such modified tetrahydropyrans include but are not limited to hexitol nucleic acid (“HNA”), anitol nucleic acid (“ANA”), manitol nucleic acid (“MNA”) (see e.g., Leumann, C J. Bioorg. & Med. Chem. 2002, 10, 841-854), fluoro HNA:
  • Figure US20220241320A1-20220804-C00010
  • (“F-HNA”, see e.g., Swayze et al., U.S. Pat. No. 8,088,904; Swayze et al., U.S. Pat. No. 8,440,803; and Swayze et al., U.S. Pat. No. 9,005,906, F-HNA can also be referred to as a F-THP or 3′-fluoro tetrahydropyran), and nucleosides comprising additional modified THP compounds having the formula:
  • Figure US20220241320A1-20220804-C00011
  • wherein, independently, for each of said modified THP nucleoside:
  • Bx is a nucleobase moiety;
  • T3 and T4 are each, independently, an internucleoside linking group linking the modified THP nucleoside to the remainder of an oligonucleotide or one of T3 and T4 is an internucleoside linking group linking the modified THP nucleoside to the remainder of an oligonucleotide and the other of T3 and T4 is H, a hydroxyl protecting group, a linked conjugate group, or a 5′ or 3′-terminal group; q1, q2, q3, q4, q5, q6 and q7 are each, independently, H, C1-C6 alkyl, substituted C1-C6 alkyl, C2-C6 alkenyl, substituted C2-C6 alkenyl, C2-C6 alkynyl, or substituted C2-C6 alkynyl; and each of R1 and R2 is independently selected from among: hydrogen, halogen, substituted or unsubstituted alkoxy, NJ1J2, SJ1, N3, OC(═X)J1, OC(═X)NJ1J2, NJ3C(═X)NJ1J2, and CN, wherein X is O, S or NJ1, and each J1, J2, and J3 is, independently, H or C1-C6 alkyl.
  • In certain embodiments, modified THP nucleosides are provided wherein q1, q2, q3, q4, q5, q6 and q7 are each H. In certain embodiments, at least one of q1, q2, q3, q4, q5, q6 and q7 is other than H. In certain embodiments, at least one of q1, q2, q3, q4, q5, q6 and q7 is methyl. In certain embodiments, modified THP nucleosides are provided wherein one of R1 and R2 is F. In certain embodiments, R1 is F and R2 is H, in certain embodiments, R1 is methoxy and R2 is H, and in certain embodiments, R1 is methoxyethoxy and R2 is H.
  • In certain embodiments, sugar surrogates comprise rings having more than 5 atoms and more than one heteroatom. For example, nucleosides comprising morpholino sugar moieties and their use in oligonucleotides have been reported (see, e.g., Braasch et al., Biochemistry, 2002, 41, 4503-4510 and Summerton et al., U.S. Pat. No. 5,698,685; Summerton et al., U.S. Pat. No. 5,166,315; Summerton et al., U.S. Pat. No. 5,185,444; and Summerton et al., U.S. 5,034,506). As used here, the term “morpholino” means a sugar surrogate having the following structure:
  • Figure US20220241320A1-20220804-C00012
  • In certain embodiments, morpholinos may be modified, for example by adding or altering various substituent groups from the above morpholino structure. Such sugar surrogates are referred to herein as “modified morpholinos.”
  • In certain embodiments, sugar surrogates comprise acyclic moieties. Examples of nucleosides and oligonucleotides comprising such acyclic sugar surrogates include but are not limited to: peptide nucleic acid (“PNA”), acyclic butyl nucleic acid (see, e.g., Kumar et al., Org. Biomol. Chem., 2013, 11, 5853-5865), and nucleosides and oligonucleotides described in Manoharan et al., US2013/130378.
  • Many other bicyclic and tricyclic sugar and sugar surrogate ring systems are known in the art that can be used in modified nucleosides.
  • 2. Modified Nucleobases
  • Nucleobase (or base) modifications or substitutions are structurally distinguishable from, yet functionally interchangeable with, naturally occurring or synthetic unmodified nucleobases. Both natural and modified nucleobases are capable of participating in hydrogen bonding. Such nucleobase modifications can impart nuclease stability, binding affinity or some other beneficial biological property to antisense compounds.
  • In certain embodiments, compounds described herein comprise modified oligonucleotides. In certain embodiments, modified oligonucleotides comprise one or more nucleoside comprising an unmodified nucleobase. In certain embodiments, modified oligonucleotides comprise one or more nucleoside comprising a modified nucleobase. In certain embodiments, modified oligonucleotides comprise one or more nucleoside that does not comprise a nucleobase, referred to as an abasic nucleoside.
  • In certain embodiments, modified nucleobases are selected from: 5-substituted pyrimidines, 6-azapyrimidines, alkyl or alkynyl substituted pyrimidines, alkyl substituted purines, and N-2, N-6 and 0-6 substituted purines. In certain embodiments, modified nucleobases are selected from: 2-aminopropyladenine, 5-hydroxymethyl cytosine, 5-methylcytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-N-methylguanine, 6-N-methyladenine, 2-propyladenine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-propynyl (C═C—CH3) uracil, 5-propynylcytosine, 6-azouracil, 6-azocytosine, 6-azothymine, 5-ribosyluracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl, 8-aza and other 8-substituted purines, 5-halo, particularly 5-bromo, 5-trifluoromethyl, 5-halouracil, and 5-halocytosine, 7-methylguanine, 7-methyladenine, 2-F-adenine, 2-aminoadenine, 7-deazaguanine, 7-deazaadenine, 3-deazaguanine, 3-deazaadenine, 6-N-benzoyladenine, 2-N-isobutyrylguanine, 4-N-benzoylcytosine, 4-N-benzoyluracil, 5-methyl 4-N-benzoylcytosine, 5-methyl 4-N-benzoyluracil, universal bases, hydrophobic bases, promiscuous bases, size-expanded bases, and fluorinated bases. Further modified nucleobases include tricyclic pyrimidines, such as 1,3-diazaphenoxazine-2-one, 1,3-diazaphenothiazine-2-one and 9-(2-aminoethoxy)-1,3-diazaphenoxazine-2-one (G-clamp). Modified nucleobases may also include those in which the purine or pyrimidine base is replaced with other heterocycles, for example 7-deaza-adenine, 7-deazaguanosine, 2-aminopyridine and 2-pyridone. Further nucleobases include those disclosed in Merigan et al., U.S. Pat. No. 3,687,808, those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering, Kroschwitz, J. I., Ed., John Wiley & Sons, 1990, 858-859; Englisch et al., Angewandte Chemie, International Edition, 1991, 30, 613; Sanghvi, Y. S., Chapter 15, Antisense Research and Applications, Crooke, S. T. and Lebleu, B., Eds., CRC Press, 1993, 273-288; and those disclosed in Chapters 6 and 15, Antisense Drug Technology, Crooke S. T., Ed., CRC Press, 2008, 163-166 and 442-443.
  • Publications that teach the preparation of certain of the above noted modified nucleobases as well as other modified nucleobases include without limitation, Manoharan et al., US2003/0158403, Manoharan et al., US2003/0175906; Dinh et al., U.S. Pat. No. 4,845,205; Spielvogel et al., U.S. Pat. No. 5,130,302; Rogers et al., U.S. Pat. No. 5,134,066; Bischofberger et al., U.S. Pat. No. 5,175,273; Urdea et al., U.S. Pat. No. 5,367,066; Benner et al., U.S. Pat. No. 5,432,272; Matteucci et al., U.S. Pat. No. 5,434,257; Gmeiner et al., U.S. Pat. No. 5,457,187; Cook et al., U.S. Pat. No. 5,459,255; Froehler et al., U.S. Pat. No. 5,484,908; Matteucci et al., U.S. Pat. No. 5,502,177; Hawkins et al., U.S. Pat. No. 5,525,711; Haralambidis et al., U.S. Pat. No. 5,552,540; Cook et al., U.S. Pat. No. 5,587,469; Froehler et al., U.S. Pat. No. 5,594,121; Switzer et al., U.S. Pat. No. 5,596,091; Cook et al., U.S. Pat. No. 5,614,617; Froehler et al., U.S. Pat. No. 5,645,985; Cook et al., U.S. Pat. No. 5,681,941; Cook et al., U.S. Pat. No. 5,811,534; Cook et al., U.S. Pat. No. 5,750,692; Cook et al., U.S. Pat. No. 5,948,903; Cook et al., U.S. Pat. No. 5,587,470; Cook et al., U.S. Pat. No. 5,457,191; Matteucci et al., U.S. Pat. No. 5,763,588; Froehler et al., U.S. Pat. No. 5,830,653; Cook et al., U.S. Pat. No. 5,808,027; Cook et al., U.S. Pat. No. 6,166,199; and Matteucci et al., U.S. Pat. No. 6,005,096.
  • In certain embodiments, compounds targeted to a IRF4 nucleic acid comprise one or more modified nucleobases. In certain embodiments, the modified nucleobase is 5-methylcytosine. In certain embodiments, each cytosine is a 5-methylcytosine.
  • 3. Modified Internucleoside Linkages
  • The naturally occurring internucleoside linkage of RNA and DNA is a 3′ to 5′ phosphodiester linkage In certain embodiments, compounds described herein having one or more modified, i.e. non-naturally occurring, internucleoside linkages are often selected over compounds having naturally occurring internucleoside linkages because of desirable properties such as, for example, enhanced cellular uptake, enhanced affinity for target nucleic acids, and increased stability in the presence of nucleases.
  • Representative internucleoside linkages having a chiral center include but are not limited to alkylphosphonates and phosphorothioates. Modified oligonucleotides comprising internucleoside linkages having a chiral center can be prepared as populations of modified oligonucleotides comprising stereorandom internucleoside linkages, or as populations of modified oligonucleotides comprising phosphorothioate linkages in particular stereochemical configurations. In certain embodiments, populations of modified oligonucleotides comprise phosphorothioate internucleoside linkages wherein all of the phosphorothioate internucleoside linkages are stereorandom. Such modified oligonucleotides can be generated using synthetic methods that result in random selection of the stereochemical configuration of each phosphorothioate linkage. Nonetheless, as is well understood by those of skill in the art, each individual phosphorothioate of each individual oligonucleotide molecule has a defined stereoconfiguration. In certain embodiments, populations of modified oligonucleotides are enriched for modified oligonucleotides comprising one or more particular phosphorothioate internucleoside linkages in a particular, independently selected stereochemical configuration. In certain embodiments, the particular configuration of the particular phosphorothioate linkage is present in at least 65% of the molecules in the population. In certain embodiments, the particular configuration of the particular phosphorothioate linkage is present in at least 70% of the molecules in the population. In certain embodiments, the particular configuration of the particular phosphorothioate linkage is present in at least 80% of the molecules in the population. In certain embodiments, the particular configuration of the particular phosphorothioate linkage is present in at least 90% of the molecules in the population. In certain embodiments, the particular configuration of the particular phosphorothioate linkage is present in at least 99% of the molecules in the population. Such chirally enriched populations of modified oligonucleotides can be generated using synthetic methods known in the art, e.g., methods described in Oka et al., JACS 125, 8307 (2003), Wan et al. Nuc. Acid. Res. 42, 13456 (2014), and WO 2017/015555. In certain embodiments, a population of modified oligonucleotides is enriched for modified oligonucleotides having at least one indicated phosphorothioate in the (Sp) configuration. In certain embodiments, a population of modified oligonucleotides is enriched for modified oligonucleotides having at least one phosphorothioate in the (Rp) configuration. In certain embodiments, modified oligonucleotides comprising (Rp) and/or (Sp) phosphorothioates comprise one or more of the following formulas, respectively, wherein “B” indicates a nucleobase:
  • Figure US20220241320A1-20220804-C00013
  • Unless otherwise indicated, chiral internucleoside linkages of modified oligonucleotides described herein can be stereorandom or in a particular stereochemical configuration.
  • In certain embodiments, compounds targeted to an IRF4 nucleic acid comprise one or more modified internucleoside linkages. In certain embodiments, the modified internucleoside linkages are phosphorothioate linkages. In certain embodiments, each internucleoside linkage of an antisense compound is a phosphorothioate internucleoside linkage.
  • In certain embodiments, compounds described herein comprise oligonucleotides. Oligonucleotides having modified internucleoside linkages include internucleoside linkages that retain a phosphorus atom as well as internucleoside linkages that do not have a phosphorus atom. Representative phosphorus containing internucleoside linkages include, but are not limited to, phosphodiesters, phosphotriesters, methylphosphonates, phosphoramidate, and phosphorothioates. Methods of preparation of phosphorous-containing and non-phosphorous-containing linkages are well known.
  • In certain embodiments, nucleosides of modified oligonucleotides may be linked together using any internucleoside linkage. The two main classes of internucleoside linking groups are defined by the presence or absence of a phosphorus atom. Representative phosphorus-containing internucleoside linkages include but are not limited to phosphates, which contain a phosphodiester bond (“P═O”) (also referred to as unmodified or naturally occurring linkages), phosphotriesters, methylphosphonates, phosphoramidates, and phosphorothioates (“P═S”), and phosphorodithioates (“HS-P═S”). Representative non-phosphorus containing internucleoside linking groups include but are not limited to methylenemethylimino (—CH2-N(CH3)-O—CH2-), thiodiester, thionocarbamate (—O—C(═O)(NH)—S—); siloxane (—O—SiH2-O—); and N,N′-dimethylhydrazine (—CH2-N(CH3)-N(CH3)-). Modified internucleoside linkages, compared to naturally occurring phosphate linkages, can be used to alter, typically increase, nuclease resistance of the oligonucleotide. In certain embodiments, internucleoside linkages having a chiral atom can be prepared as a racemic mixture, or as separate enantiomers. Representative chiral internucleoside linkages include but are not limited to alkylphosphonates and phosphorothioates. Methods of preparation of phosphorous-containing and non-phosphorous-containing internucleoside linkages are well known to those skilled in the art.
  • Neutral internucleoside linkages include, without limitation, phosphotriesters, methylphosphonates, MMI (3′-CH2—N(CH3)-O-5′), amide-3 (3′-CH2-C(═O)—N(H)-5′), amide-4 (3′-CH2-N(H)—C(═O)-5′), formacetal (3′-O-CH2-O-5′), methoxypropyl, and thioformacetal (3′-S—CH2-O-5′). Further neutral internucleoside linkages include nonionic linkages comprising siloxane (dialkylsiloxane), carboxylate ester, carboxamide, sulfide, sulfonate ester and amides (See for example: Carbohydrate Modifications in Antisense Research; Y. S. Sanghvi and P. D. Cook, Eds., ACS Symposium Series 580; Chapters 3 and 4, 40-65). Further neutral internucleoside linkages include nonionic linkages comprising mixed N, O, S and CH2 component parts.
  • In certain embodiments, oligonucleotides comprise modified internucleoside linkages arranged along the oligonucleotide or region thereof in a defined pattern or modified internucleoside linkage motif. In certain embodiments, internucleoside linkages are arranged in a gapped motif. In such embodiments, the internucleoside linkages in each of two wing regions are different from the internucleoside linkages in the gap region. In certain embodiments the internucleoside linkages in the wings are phosphodiester and the internucleoside linkages in the gap are phosphorothioate. The nucleoside motif is independently selected, so such oligonucleotides having a gapped internucleoside linkage motif may or may not have a gapped nucleoside motif and if it does have a gapped nucleoside motif, the wing and gap lengths may or may not be the same.
  • In certain embodiments, oligonucleotides comprise a region having an alternating internucleoside linkage motif. In certain embodiments, oligonucleotides comprise a region of uniformly modified internucleoside linkages. In certain such embodiments, the oligonucleotide comprises a region that is uniformly linked by phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide is uniformly linked by phosphorothioate. In certain embodiments, each internucleoside linkage of the oligonucleotide is selected from phosphodiester and phosphorothioate. In certain embodiments, each internucleoside linkage of the oligonucleotide is selected from phosphodiester and phosphorothioate and at least one internucleoside linkage is phosphorothioate.
  • In certain embodiments, the oligonucleotide comprises at least 6 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least 8 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least 10 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least one block of at least 6 consecutive phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least one block of at least 8 consecutive phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least one block of at least 10 consecutive phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least block of at least one 12 consecutive phosphorothioate internucleoside linkages. In certain such embodiments, at least one such block is located at the 3′ end of the oligonucleotide. In certain such embodiments, at least one such block is located within 3 nucleosides of the 3′ end of the oligonucleotide.
  • In certain embodiments, oligonucleotides comprise one or more methylphosphonate linkages. In certain embodiments, oligonucleotides having a gapmer nucleoside motif comprise a linkage motif comprising all phosphorothioate linkages except for one or two methylphosphonate linkages. In certain embodiments, one methylphosphonate linkage is in the central gap of an oligonucleotide having a gapmer nucleoside motif.
  • In certain embodiments, it is desirable to arrange the number of phosphorothioate internucleoside linkages and phosphodiester internucleoside linkages to maintain nuclease resistance. In certain embodiments, it is desirable to arrange the number and position of phosphorothioate internucleoside linkages and the number and position of phosphodiester internucleoside linkages to maintain nuclease resistance. In certain embodiments, the number of phosphorothioate internucleoside linkages may be decreased and the number of phosphodiester internucleoside linkages may be increased. In certain embodiments, the number of phosphorothioate internucleoside linkages may be decreased and the number of phosphodiester internucleoside linkages may be increased while still maintaining nuclease resistance. In certain embodiments it is desirable to decrease the number of phosphorothioate internucleoside linkages while retaining nuclease resistance. In certain embodiments it is desirable to increase the number of phosphodiester internucleoside linkages while retaining nuclease resistance.
  • Certain Motifs
  • In certain embodiments, compounds described herein comprise oligonucleotides. Oligonucleotides can have a motif, e.g. a pattern of unmodified and/or modified sugar moieties, nucleobases, and/or internucleoside linkages. In certain embodiments, modified oligonucleotides comprise one or more modified nucleoside comprising a modified sugar. In certain embodiments, modified oligonucleotides comprise one or more modified nucleosides comprising a modified nucleobase. In certain embodiments, modified oligonucleotides comprise one or more modified internucleoside linkage. In such embodiments, the modified, unmodified, and differently modified sugar moieties, nucleobases, and/or internucleoside linkages of a modified oligonucleotide define a pattern or motif. In certain embodiments, the patterns of sugar moieties, nucleobases, and internucleoside linkages are each independent of one another. Thus, a modified oligonucleotide may be described by its sugar motif, nucleobase motif and/or internucleoside linkage motif (as used herein, nucleobase motif describes the modifications to the nucleobases independent of the sequence of nucleobases).
  • a. Certain Sugar Motifs
  • In certain embodiments, compounds described herein comprise oligonucleotides. In certain embodiments, oligonucleotides comprise one or more type of modified sugar and/or unmodified sugar moiety arranged along the oligonucleotide or region thereof in a defined pattern or sugar motif. In certain instances, such sugar motifs include but are not limited to any of the sugar modifications discussed herein.
  • In certain embodiments, modified oligonucleotides comprise or consist of a region having a gapmer motif, which comprises two external regions or “wings” and a central or internal region or “gap.” The three regions of a gapmer motif (the 5′-wing, the gap, and the 3′-wing) form a contiguous sequence of nucleosides wherein at least some of the sugar moieties of the nucleosides of each of the wings differ from at least some of the sugar moieties of the nucleosides of the gap. Specifically, at least the sugar moieties of the nucleosides of each wing that are closest to the gap (the 3′-most nucleoside of the 5′-wing and the 5′-most nucleoside of the 3′-wing) differ from the sugar moiety of the neighboring gap nucleosides, thus defining the boundary between the wings and the gap (i.e., the wing/gap junction). In certain embodiments, the sugar moieties within the gap are the same as one another. In certain embodiments, the gap includes one or more nucleoside having a sugar moiety that differs from the sugar moiety of one or more other nucleosides of the gap. In certain embodiments, the sugar motifs of the two wings are the same as one another (symmetric gapmer). In certain embodiments, the sugar motif of the 5′-wing differs from the sugar motif of the 3′-wing (asymmetric gapmer).
  • In certain embodiments, the wings of a gapmer comprise 1-5 nucleosides. In certain embodiments, the wings of a gapmer comprise 2-5 nucleosides. In certain embodiments, the wings of a gapmer comprise 3-5 nucleosides. In certain embodiments, the nucleosides of a gapmer are all modified nucleosides.
  • In certain embodiments, the gap of a gapmer comprises 7-12 nucleosides. In certain embodiments, the gap of a gapmer comprises 7-10 nucleosides. In certain embodiments, the gap of a gapmer comprises 8-10 nucleosides. In certain embodiments, the gap of a gapmer comprises 10 nucleosides. In certain embodiment, each nucleoside of the gap of a gapmer is an unmodified 2′-deoxy nucleoside.
  • In certain embodiments, the gapmer is a deoxy gapmer. In such embodiments, the nucleosides on the gap side of each wing/gap junction are unmodified 2′-deoxy nucleosides and the nucleosides on the wing sides of each wing/gap junction are modified nucleosides. In certain such embodiments, each nucleoside of the gap is an unmodified 2′-deoxy nucleoside. In certain such embodiments, each nucleoside of each wing is a modified nucleoside.
  • In certain embodiments, a modified oligonucleotide has a fully modified sugar motif wherein each nucleoside of the modified oligonucleotide comprises a modified sugar moiety. In certain embodiments, modified oligonucleotides comprise or consist of a region having a fully modified sugar motif wherein each nucleoside of the region comprises a modified sugar moiety. In certain embodiments, modified oligonucleotides comprise or consist of a region having a fully modified sugar motif, wherein each nucleoside within the fully modified region comprises the same modified sugar moiety, referred to herein as a uniformly modified sugar motif. In certain embodiments, a fully modified oligonucleotide is a uniformly modified oligonucleotide. In certain embodiments, each nucleoside of a uniformly modified comprises the same 2′-modification.
  • In certain embodiments, a modified oligonucleotide can comprise a sugar motif described in Swayze et al., US2010/0197762; Freier et al., US2014/0107330; Freier et al., US2015/0184153; and Seth et al., US2015/0267195, each of which is incorporated by reference in its entirety herein.
  • Certain embodiments provided herein are directed to modified oligomeric compounds useful for inhibiting target nucleic acid expression, which can be useful for treating, preventing, ameliorating, or slowing progression of a disease associated with such a target nucleic acid. In certain embodiments, the modified oligomeric compounds comprise antisense oligonucleotides that are gapmers having certain sugar motifs. In certain embodiments, the gapmer sugar motifs provided herein can be combined with any nucleobase sequence and any internucleoside linkage motif to form potent antisense oligonucleotides.
  • In certain embodiments, a method comprises contacting a cell or administering to a subject a compound comprising a modified oligonucleotide 16 linked nucleosides in length having the motif: ekk-d9-kkee, wherein ‘d’ represents a 2′-deoxyribose sugar, ‘k’ represents a cEt nucleoside, and ‘e’ represents a 2′-MOE nucleoside. In certain embodiments, the cell is a cancer cell. In certain embodiments, the subject has cancer. In certain embodiments, administering the compound to the subject treats the subject's cancer.
  • In certain embodiments, a method comprises contacting a cell or administering to a subject a compound comprising a modified oligonucleotide 16 linked nucleosides in length having the motif: k-d9-kekeke, wherein represents a 2′-deoxyribose sugar, ‘k’ represents a cEt nucleoside, and ‘e’ represents a 2′-MOE nucleoside. In certain embodiments, the cell is a cancer cell. In certain embodiments, the subject has cancer. In certain embodiments, administering the compound to the subject treats the subject's cancer.
  • In certain embodiments, a method comprises contacting a cell or administering to a subject a compound comprising a modified oligonucleotide 16 linked nucleosides in length having the motif: kkk-d8-kekek, wherein ‘d’ represents a 2′-deoxyribose sugar, ‘k’ represents a cEt nucleoside, and ‘e’ represents a 2′-MOE nucleoside. In certain embodiments, the cell is a cancer cell. In certain embodiments, the subject has cancer. In certain embodiments, administering the compound to the subject treats the subject's cancer.
  • In certain embodiments, a method comprises contacting a cell or administering to a subject a compound comprising a modified oligonucleotide 16 linked nucleosides in length having the motif: kkk-d9-keke, wherein ‘d’ represents a 2′-deoxyribose sugar, ‘k’ represents a cEt nucleoside, and ‘e’ represents a 2′-MOE nucleoside. In certain embodiments, the cell is a cancer cell. In certain embodiments, the subject has cancer. In certain embodiments, administering the compound to the subject treats the subject's cancer.
  • In certain embodiments, a method comprises contacting a cell or administering to a subject a compound comprising a modified oligonucleotide 16 linked nucleosides in length having the motif: kk-d9-kdkdk, wherein ‘d’ represents a 2′-deoxyribose sugar, ‘k’ represents a cEt nucleoside, and ‘e’ represents a 2′-MOE nucleoside. In certain embodiments, the cell is a cancer cell. In certain embodiments, the subject has cancer. In certain embodiments, administering the compound to the subject treats the subject's cancer.
  • In certain embodiments, a compound comprises a modified oligonucleotide 16 linked nucleosides in length having the motif: kk-d9-eeekk, wherein ‘d’ represents a 2′-deoxyribose sugar, ‘k’ represents a cEt nucleoside, and ‘e’ represents a 2′-MOE nucleoside. In certain embodiments, a method comprises contacting a cell or administering to a subject a compound comprising a modified oligonucleotide 16 linked nucleosides in length having the motif: kk-d9-eeekk, wherein ‘d’ represents a 2′-deoxyribose sugar, ‘k’ represents a cEt nucleoside, and ‘e’ represents a 2′-MOE nucleoside. In certain embodiments, the cell is a cancer cell. In certain embodiments, the subject has cancer. In certain embodiments, administering the compound to the subject treats the subject's cancer.
  • In certain embodiments, a method comprises contacting a cell or administering to a subject a compound comprising a modified oligonucleotide 16 linked nucleosides in length having the motif: kk-d9-kdkdk, wherein ‘d’ represents a 2′-deoxyribose sugar, ‘k’ represents a cEt nucleoside, and ‘e’ represents a 2′-MOE nucleoside. In certain embodiments, the cell is a cancer cell. In certain embodiments, the subject has cancer. In certain embodiments, administering the compound to the subject treats the subject's cancer.
  • b. Certain Nucleobase Motifs
  • In certain embodiments, compounds described herein comprise oligonucleotides. In certain embodiments, oligonucleotides comprise modified and/or unmodified nucleobases arranged along the oligonucleotide or region thereof in a defined pattern or motif. In certain embodiments, each nucleobase is modified. In certain embodiments, none of the nucleobases are modified. In certain embodiments, each purine or each pyrimidine is modified. In certain embodiments, each adenine is modified. In certain embodiments, each guanine is modified. In certain embodiments, each thymine is modified. In certain embodiments, each uracil is modified. In certain embodiments, each cytosine is modified. In certain embodiments, some or all of the cytosine nucleobases in a modified oligonucleotide are 5-methylcytosines.
  • In certain embodiments, modified oligonucleotides comprise a block of modified nucleobases. In certain such embodiments, the block is at the 3′-end of the oligonucleotide. In certain embodiments the block is within 3 nucleosides of the 3′-end of the oligonucleotide. In certain embodiments, the block is at the 5′-end of the oligonucleotide. In certain embodiments the block is within 3 nucleosides of the 5′-end of the oligonucleotide.
  • In certain embodiments, oligonucleotides having a gapmer motif comprise a nucleoside comprising a modified nucleobase. In certain such embodiments, one nucleoside comprising a modified nucleobase is in the central gap of an oligonucleotide having a gapmer motif. In certain such embodiments, the sugar moiety of said nucleoside is a 2′-deoxyribosyl moiety. In certain embodiments, the modified nucleobase is selected from: a 2-thiopyrimidine and a 5-propynepyrimidine.
  • c. Certain Internucleoside Linkage Motifs
  • In certain embodiments, compounds described herein comprise oligonucleotides. In certain embodiments, oligonucleotides comprise modified and/or unmodified internucleoside linkages arranged along the oligonucleotide or region thereof in a defined pattern or motif. In certain embodiments, essentially each internucleoside linking group is a phosphate internucleoside linkage (P═O). In certain embodiments, each internucleoside linking group of a modified oligonucleotide is a phosphorothioate (P═S). In certain embodiments, each internucleoside linking group of a modified oligonucleotide is independently selected from a phosphorothioate and phosphate internucleoside linkage. In certain embodiments, the sugar motif of a modified oligonucleotide is a gapmer and the internucleoside linkages within the gap are all modified. In certain such embodiments, some or all of the internucleoside linkages in the wings are unmodified phosphate linkages. In certain embodiments, the terminal internucleoside linkages are modified.
  • 4. Certain Modified Oligonucleotides
  • In certain embodiments, compounds described herein comprise modified oligonucleotides. In certain embodiments, the above modifications (sugar, nucleobase, internucleoside linkage) are incorporated into a modified oligonucleotide. In certain embodiments, modified oligonucleotides are characterized by their modification, motifs, and overall lengths. In certain embodiments, such parameters are each independent of one another. Thus, unless otherwise indicated, each internucleoside linkage of an oligonucleotide having a gapmer sugar motif may be modified or unmodified and may or may not follow the gapmer modification pattern of the sugar modifications. For example, the internucleoside linkages within the wing regions of a sugar gapmer may be the same or different from one another and may be the same or different from the internucleoside linkages of the gap region of the sugar motif. Likewise, such gapmer oligonucleotides may comprise one or more modified nucleobase independent of the gapmer pattern of the sugar modifications. Furthermore, in certain instances, an oligonucleotide is described by an overall length or range and by lengths or length ranges of two or more regions (e.g., a regions of nucleosides having specified sugar modifications), in such circumstances it may be possible to select numbers for each range that result in an oligonucleotide having an overall length falling outside the specified range. In such circumstances, both elements must be satisfied. For example, in certain embodiments, a modified oligonucleotide consists of 15-20 linked nucleosides and has a sugar motif consisting of three regions, A, B, and C, wherein region A consists of 2-6 linked nucleosides having a specified sugar motif, region B consists of 6-10 linked nucleosides having a specified sugar motif, and region C consists of 2-6 linked nucleosides having a specified sugar motif. Such embodiments do not include modified oligonucleotides where A and C each consist of 6 linked nucleosides and B consists of 10 linked nucleosides (even though those numbers of nucleosides are permitted within the requirements for A, B, and C) because the overall length of such oligonucleotide is 22, which exceeds the upper limit of the overall length of the modified oligonucleotide (20). Herein, if a description of an oligonucleotide is silent with respect to one or more parameter, such parameter is not limited. Thus, a modified oligonucleotide described only as having a gapmer sugar motif without further description may have any length, internucleoside linkage motif, and nucleobase motif. Unless otherwise indicated, all modifications are independent of nucleobase sequence.
  • Certain Conjugated Compounds
  • In certain embodiments, the compounds described herein comprise or consist of an oligonucleotide (modified or unmodified) and optionally one or more conjugate groups and/or terminal groups. Conjugate groups consist of one or more conjugate moiety and a conjugate linker which links the conjugate moiety to the oligonucleotide. Conjugate groups may be attached to either or both ends of an oligonucleotide and/or at any internal position. In certain embodiments, conjugate groups are attached to the 2′-position of a nucleoside of a modified oligonucleotide. In certain embodiments, conjugate groups that are attached to either or both ends of an oligonucleotide are terminal groups. In certain such embodiments, conjugate groups or terminal groups are attached at the 3′ and/or 5′-end of oligonucleotides. In certain such embodiments, conjugate groups (or terminal groups) are attached at the 3′-end of oligonucleotides. In certain embodiments, conjugate groups are attached near the 3′-end of oligonucleotides. In certain embodiments, conjugate groups (or terminal groups) are attached at the 5′-end of oligonucleotides. In certain embodiments, conjugate groups are attached near the 5′-end of oligonucleotides.
  • In certain embodiments, the oligonucleotide is modified. In certain embodiments, the oligonucleotide of a compound has a nucleobase sequence that is complementary to a target nucleic acid. In certain embodiments, oligonucleotides are complementary to a messenger RNA (mRNA). In certain embodiments, oligonucleotides are complementary to a sense transcript.
  • Examples of terminal groups include but are not limited to conjugate groups, capping groups, phosphate moieties, protecting groups, modified or unmodified nucleosides, and two or more nucleosides that are independently modified or unmodified.
  • A. Certain Conjugate Groups
  • In certain embodiments, oligonucleotides are covalently attached to one or more conjugate groups. In certain embodiments, conjugate groups modify one or more properties of the attached oligonucleotide, including but not limited to pharmacodynamics, pharmacokinetics, stability, binding, absorption, tissue distribution, cellular distribution, cellular uptake, charge and clearanceln certain embodiments, conjugate groups impart a new property on the attached oligonucleotide, e.g., fluorophores or reporter groups that enable detection of the oligonucleotide.
  • Certain conjugate groups and conjugate moieties have been described previously, for example: cholesterol moiety (Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989, 86, 6553-6556), cholic acid (Manoharan et al., Bioorg. Med. Chem. Lett., 1994, 4, 1053-1060), a thioether, e.g., hexyl-S-tritylthiol (Manoharan et al., Ann. N.Y. Acad. Sci., 1992, 660, 306-309; Manoharan et al., Bioorg. Med. Chem. Lett., 1993, 3, 2765-2770), a thiocholesterol (Oberhauser et al., Nucl. Acids Res., 1992, 20, 533-538), an aliphatic chain, e.g., do-decan-diol or undecyl residues (Saison-Behmoaras et al., EMBO J., 1991, 10, 1111-1118; Kabanov et al., FEBS Lett., 1990, 259, 327-330; Svinarchuk et al., Biochimie, 1993, 75, 49-54), a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethyl-ammonium 1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651-3654; Shea et al., Nucl. Acids Res., 1990, 18, 3777-3783), a polyamine or a polyethylene glycol chain (Manoharan et al., Nucleosides & Nucleotides, 1995, 14, 969-973), or adamantane acetic, a palmityl moiety (Mishra et al., Biochim. Biophys. Acta, 1995, 1264, 229-237), an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety (Crooke et al., J. Pharmacol. Exp. Ther., 1996, i, 923-937), a tocopherol group (Nishina et al., Molecular Therapy Nucleic Acids, 2015, 4, e220; doi:10.1038/mtna.2014.72 and Nishina et al., Molecular Therapy, 2008, 16, 734-740), or a GalNAc cluster (e.g., WO2014/179620).
  • 1. Conjugate Moieties
  • Conjugate moieties include, without limitation, intercalators, reporter molecules, polyamines, polyamides, peptides, carbohydrates (e.g., GalNAc), vitamin moieties, polyethylene glycols, thioethers, polyethers, cholesterols, thiocholesterols, cholic acid moieties, folate, lipids, phospholipids, biotin, phenazine, phenanthridine, anthraquinone, adamantane, acridine, fluoresceins, rhodamines, coumarins, fluorophores, and dyes.
  • In certain embodiments, a conjugate moiety comprises an active drug substance, for example, aspirin, warfarin, phenylbutazone, ibuprofen, suprofen, fen-bufen, ketoprofen, (S)-(±)-pranoprofen, carprofen, dansylsarcosine, 2,3,5-triiodobenzoic acid, fingolimod, flufenamic acid, folinic acid, a benzothiadiazide, chlorothiazide, a diazepine, indo-methicin, a barbiturate, a cephalosporin, a sulfa drug, an antidiabetic, an antibacterial or an antibiotic.
  • 2. Conjugate Linkers
  • Conjugate moieties are attached to oligonucleotides through conjugate linkers. In certain compounds, a conjugate group is a single chemical bond (i.e. conjugate moiety is attached to an oligonucleotide via a conjugate linker through a single bond). In certain embodiments, the conjugate linker comprises a chain structure, such as a hydrocarbyl chain, or an oligomer of repeating units such as ethylene glycol, nucleosides, or amino acid units.
  • In certain embodiments, a conjugate linker comprises one or more groups selected from alkyl, amino, oxo, amide, disulfide, polyethylene glycol, ether, thioether, and hydroxylamino. In certain such embodiments, the conjugate linker comprises groups selected from alkyl, amino, oxo, amide and ether groups. In certain embodiments, the conjugate linker comprises groups selected from alkyl and amide groups. In certain embodiments, the conjugate linker comprises groups selected from alkyl and ether groups. In certain embodiments, the conjugate linker comprises at least one phosphorus moiety. In certain embodiments, the conjugate linker comprises at least one phosphate group. In certain embodiments, the conjugate linker includes at least one neutral linking group.
  • In certain embodiments, conjugate linkers, including the conjugate linkers described above, are bifunctional linking moieties, e.g., those known in the art to be useful for attaching conjugate groups to parent compounds, such as the oligonucleotides provided herein. In general, a bifunctional linking moiety comprises at least two functional groups. One of the functional groups is selected to bind to a particular site on a compound and the other is selected to bind to a conjugate group. Examples of functional groups used in a bifunctional linking moiety include but are not limited to electrophiles for reacting with nucleophilic groups and nucleophiles for reacting with electrophilic groups. In certain embodiments, bifunctional linking moieties comprise one or more groups selected from amino, hydroxyl, carboxylic acid, thiol, alkyl, alkenyl, and alkynyl.
  • Examples of conjugate linkers include but are not limited to pyrrolidine, 8-amino-3,6-dioxaoctanoic acid (ADO), succinimidyl 4-(N-maleimidomethyl) cyclohexane-1-carboxylate (SMCC) and 6-aminohexanoic acid (AHEX or AHA). Other conjugate linkers include but are not limited to substituted or unsubstituted C1-C10 alkyl, substituted or unsubstituted C2-C10 alkenyl or substituted or unsubstituted C2-C10 alkynyl, wherein a nonlimiting list of preferred substituent groups includes hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro, thiol, thioalkoxy, halogen, alkyl, aryl, alkenyl and alkynyl.
  • In certain embodiments, conjugate linkers comprise 1-10 linker-nucleosides. In certain embodiments, such linker-nucleosides are modified nucleosides. In certain embodiments such linker-nucleosides comprise a modified sugar moiety. In certain embodiments, linker-nucleosides are unmodified. In certain embodiments, linker-nucleosides comprise an optionally protected heterocyclic base selected from a purine, substituted purine, pyrimidine or substituted pyrimidine. In certain embodiments, a cleavable moiety is a nucleoside selected from uracil, thymine, cytosine, 4-N-benzoylcytosine, 5-methylcytosine, 4-N-benzoyl-5-methylcytosine, adenine, 6-N-benzoyladenine, guanine and 2-N-isobutyrylguanine. It is typically desirable for linker-nucleosides to be cleaved from the compound after it reaches a target tissue. Accordingly, linker-nucleosides are typically linked to one another and to the remainder of the compound through cleavable bonds. In certain embodiments, such cleavable bonds are phosphodiester bonds.
  • Herein, linker-nucleosides are not considered to be part of the oligonucleotide. Accordingly, in embodiments in which a compound comprises an oligonucleotide consisting of a specified number or range of linked nucleosides and/or a specified percent complementarity to a reference nucleic acid and the compound also comprises a conjugate group comprising a conjugate linker comprising linker-nucleosides, those linker-nucleosides are not counted toward the length of the oligonucleotide and are not used in determining the percent complementarity of the oligonucleotide for the reference nucleic acid. For example, a compound may comprise (1) a modified oligonucleotide consisting of 8-30 nucleosides and (2) a conjugate group comprising 1-10 linker-nucleosides that are contiguous with the nucleosides of the modified oligonucleotide. The total number of contiguous linked nucleosides in such a compound is more than 30. Alternatively, an compound may comprise a modified oligonucleotide consisting of 8-30 nucleosides and no conjugate group. The total number of contiguous linked nucleosides in such a compound is no more than 30. Unless otherwise indicated conjugate linkers comprise no more than 10 linker-nucleosides. In certain embodiments, conjugate linkers comprise no more than 5 linker-nucleosides. In certain embodiments, conjugate linkers comprise no more than 3 linker-nucleosides. In certain embodiments, conjugate linkers comprise no more than 2 linker-nucleosides. In certain embodiments, conjugate linkers comprise no more than 1 linker-nucleoside.
  • In certain embodiments, it is desirable for a conjugate group to be cleaved from the oligonucleotide. For example, in certain circumstances compounds comprising a particular conjugate moiety are better taken up by a particular cell type, but once the compound has been taken up, it is desirable that the conjugate group be cleaved to release the unconjugated or parent oligonucleotide. Thus, certain conjugate may comprise one or more cleavable moieties, typically within the conjugate linker. In certain embodiments, a cleavable moiety is a cleavable bond. In certain embodiments, a cleavable moiety is a group of atoms comprising at least one cleavable bond. In certain embodiments, a cleavable moiety comprises a group of atoms having one, two, three, four, or more than four cleavable bonds. In certain embodiments, a cleavable moiety is selectively cleaved inside a cell or subcellular compartment, such as a lysosome. In certain embodiments, a cleavable moiety is selectively cleaved by endogenous enzymes, such as nucleases.
  • In certain embodiments, a cleavable bond is selected from among: an amide, an ester, an ether, one or both esters of a phosphodiester, a phosphate ester, a carbamate, or a disulfide. In certain embodiments, a cleavable bond is one or both of the esters of a phosphodiester. In certain embodiments, a cleavable moiety comprises a phosphate or phosphodiester. In certain embodiments, the cleavable moiety is a phosphate linkage between an oligonucleotide and a conjugate moiety or conjugate group.
  • In certain embodiments, a cleavable moiety comprises or consists of one or more linker-nucleosides. In certain such embodiments, one or more linker-nucleosides are linked to one another and/or to the remainder of the compound through cleavable bonds. In certain embodiments, such cleavable bonds are unmodified phosphodiester bonds. In certain embodiments, a cleavable moiety is 2′-deoxy nucleoside that is attached to either the 3′ or 5′-terminal nucleoside of an oligonucleotide by a phosphate internucleoside linkage and covalently attached to the remainder of the conjugate linker or conjugate moiety by a phosphate or phosphorothioate linkage. In certain such embodiments, the cleavable moiety is 2′-deoxyadenosine.
  • Compositions and Methods for Formulating Pharmaceutical Compositions
  • Compounds described herein may be admixed with pharmaceutically acceptable active or inert substances for the preparation of pharmaceutical compositions or formulations. Compositions and methods for the formulation of pharmaceutical compositions are dependent upon a number of criteria, including, but not limited to, route of administration, extent of disease, or dose to be administered.
  • Certain embodiments provide pharmaceutical compositions comprising one or more compounds or a salt thereof. In certain embodiments, the compounds are antisense compounds or oligomeric compounds. In certain embodiments, the compounds comprise or consist of a modified oligonucleotide. In certain such embodiments, the pharmaceutical composition comprises a suitable pharmaceutically acceptable diluent or carrier. In certain embodiments, a pharmaceutical composition comprises a sterile saline solution and one or more compound. In certain embodiments, such pharmaceutical composition consists of a sterile saline solution and one or more compound. In certain embodiments, the sterile saline is pharmaceutical grade saline. In certain embodiments, a pharmaceutical composition comprises one or more compound and sterile water. In certain embodiments, a pharmaceutical composition consists of one compound and sterile water. In certain embodiments, the sterile water is pharmaceutical grade water. In certain embodiments, a pharmaceutical composition comprises one or more compound and phosphate-buffered saline (PBS). In certain embodiments, a pharmaceutical composition consists of one or more compound and sterile PBS. In certain embodiments, the sterile PBS is pharmaceutical grade PBS. Compositions and methods for the formulation of pharmaceutical compositions are dependent upon a number of criteria, including, but not limited to, route of administration, extent of disease, or dose to be administered.
  • A compound described herein targeted to IRF4 nucleic acid can be utilized in pharmaceutical compositions by combining the compound with a suitable pharmaceutically acceptable diluent or carrier. In certain embodiments, a pharmaceutically acceptable diluent is water, such as sterile water suitable for injection. Accordingly, in one embodiment, employed in the methods described herein is a pharmaceutical composition comprising a compound targeted to IRF4 nucleic acid and a pharmaceutically acceptable diluent. In certain embodiments, the pharmaceutically acceptable diluent is water. In certain embodiments, the compound comprises or consists of a modified oligonucleotide provided herein.
  • Pharmaceutical compositions comprising compounds provided herein encompass any pharmaceutically acceptable salts, esters, or salts of such esters, or any other oligonucleotide which, upon administration to an animal, including a human, is capable of providing (directly or indirectly) the biologically active metabolite or residue thereof. In certain embodiments, the compounds are antisense compounds or oligomeric compounds. In certain embodiments, the compound comprises or consists of a modified oligonucleotide. Accordingly, for example, the disclosure is also drawn to pharmaceutically acceptable salts of compounds, prodrugs, pharmaceutically acceptable salts of such prodrugs, and other bioequivalents. Suitable pharmaceutically acceptable salts include, but are not limited to, sodium and potassium salts.
  • A prodrug can include the incorporation of additional nucleosides at one or both ends of a compound which are cleaved by endogenous nucleases within the body, to form the active compound. In certain embodiments, the compounds or compositions further comprise a pharmaceutically acceptable carrier or diluent.
  • EXAMPLES
  • The Examples below describe the screening process to identify lead compounds targeted to IRF4. Out of over 3,000 oligonucleotides that were screened, ION 690890, 935658, 935696, 935762, 935918, 935968, 882800, 1012795, 1014095, and 1014834 emerged as the top lead compounds. In particular, ION 935918 exhibited the best combination of properties in terms of potency and tolerability out of over 3,000 oligonucleotides.
  • Non-Limiting Disclosure and Incorporation by Reference
  • Although the sequence listing accompanying this filing identifies each sequence as either “RNA” or “DNA” as required, in reality, those sequences may be modified with any combination of chemical modifications. One of skill in the art will readily appreciate that such designation as “RNA” or “DNA” to describe modified oligonucleotides is, in certain instances, arbitrary. For example, an oligonucleotide comprising a nucleoside comprising a 2′-OH sugar moiety and a thymine base could be described as a DNA having a modified sugar (2′-OH for the natural 2′-H of DNA) or as an RNA having a modified base (thymine (methylated uracil) for natural uracil of RNA).
  • Accordingly, nucleic acid sequences provided herein, including, but not limited to those in the sequence listing, are intended to encompass nucleic acids containing any combination of natural or modified RNA and/or DNA, including, but not limited to such nucleic acids having modified nucleobases. By way of further example and without limitation, an oligonucleotide having the nucleobase sequence “ATCGATCG” encompasses any oligonucleotides having such nucleobase sequence, whether modified or unmodified, including, but not limited to, such compounds comprising RNA bases, such as those having sequence “AUCGAUCG” and those having some DNA bases and some RNA bases such as “AUCGATCG” and compounds having other modified nucleobases, such as “ATmCGAUCG,” wherein mC indicates a cytosine base comprising a methyl group at the 5-position.
  • While certain compounds, compositions and methods described herein have been described with specificity in accordance with certain embodiments, the following examples serve only to illustrate the compounds described herein and are not intended to limit the same. Each of the references recited in the present application is incorporated herein by reference in its entirety.
  • Example 1: Effect of 5-10-5 MOE Gapmers with Phosphorothioate Internucleoside Linkages on Human IRF4 In Vitro, Single Dose
  • Modified oligonucleotides complementary to a human IRF4 nucleic acid were designed and tested for their effect on IRF4 mRNA in vitro.
  • Cultured SK-MEL-28 cells at a density of 60,000 cells per well were transfected using electroporation with 20,000 nM concentration of modified oligonucleotide or no modified oligonucleotide for untreated controls. After approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by quantitative real-time PCR. Human primer probe set RTS3114 (forward sequence AAGCCTTGGCGTTCTCAGACT, designated herein as SEQ ID NO: 3386; reverse sequence TCAGCTCCTTCACGAGGATTTC, designated herein as SEQ ID NO: 3387; probe sequence CCGGCTGCACATCTGCCTGTACTACC, designated herein as SEQ ID: 3388) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN®. Results are presented in the table below as percent control of the amount of IRF4 mRNA, relative to untreated control (UTC) cells.
  • The modified oligonucleotides in Table 1 are 5-10-5 MOE gapmers. The gapmers are 20 nucleobases in length, wherein the central gap segment comprises ten 2′-deoxynucleosides and is flanked by wing segments on both the 5′ end and on the 3′ end comprising five 2′-MOE nucleosides. The sugar motif for the gapmers is (from 5′ to 3′): eeeeeddddddddddeeeee; wherein ‘d’ represents a 2′-deoxyribose sugar and ‘e’ represents a 2′-MOE modified sugar. Each internucleoside linkage is a phosphorothioate internucleoside linkage and each cytosine residue is a 5-methylcytosine. “Start Site” indicates the 5′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence. “Stop Site” indicates the 3′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Each modified oligonucleotide listed in Table 1 below is complementary to human IRF4 nucleic acid sequences SEQ ID NO: 1 or SEQ ID NO: 2, as indicated. ‘N/A’ indicates that the modified oligonucleotide is not complementary to that particular nucleic acid sequence with 100% complementarity. As shown below, modified oligonucleotides complementary to human IRF4 reduced the amount of human IRF4 mRNA.
  • TABLE 1
     Percent control of human IRF4 mRNA with 5-10-5 MOE gapmers
    with phosphorothioate internucleoside linkages
    SEQ SEQ SEQ SEQ
    ID ID ID ID
    NO: 1 NO: 1 NO: 2 NO: 2 IRF4
    Compound Start Stop Start Stop (% SEQ
    Number Site Site Site Site Sequence UTC) ID NO
    434887  164  183  5191 5210 GCAGCTCACCGCGCTCATGC 57  3
    434888  175  194  5202  5221 TTCCCGTTGCCGCAGCTCAC 34  4
    434889  190  209  5217  5236 AGCCACTGGCGGAGCTTCCC 43  5
    434890  294  313  5321  5340 TGTAGTCCTGCTTGCCCGCG 51  6
    434891  304  323  5331  5350 TCCTCGCGGTTGTAGTCCTG 53  7
    434892  330  349 N/A N/A CCCAAGCCTTGAAGAGCGCG 44  8
    434893  367  386  6846  6865 TTGTCGATGCCTTCTCGGAA 47  9
    434894  375  394  6854  6873 GGTCCGGCTTGTCGATGCCT 40 10
    434895  430  449  6909  6928 TCAAAGTCATTGCTCTTGTT 55 11
    434896  436  455  6915  6934 AGTTCCTCAAAGTCATTGCT 42 12
    434897  442  461  6921  6940 TCAACCAGTTCCTCAAAGTC 75 13
    434898  447  466  6926  6945 TCCGCTCAACCAGTTCCTCA 32 14
    434899  474  493  6953  6972 TGTACGGGTCTGAGATGTCC 44 15
    434900  532  551  7850  7869 TCCAGGGTGAGCTGCTTGGC 43 16
    434901  555  574  7873  7892 GGCTCATGGACATCTGCGGG 45 17
    434902  675  694  9165  9184 TTTCCGGGTGTGGCTGATCC 36 18
    434903  690  709  9180  9199 GACATTGGTACGGGATTTCC 38 19
    434904  732  751  9222  9241 CTGGGCCTTGCCAGTGGTGG 59 20
    434905  739  758  9229  9248 TCACAAGCTGGGCCTTGCCA 30 21
    434906  744  763  9234  9253 CATTTTCACAAGCTGGGCCT 37 22
    434907  751  770 N/A N/A TGGCAACCATTTTCACAAGC 37 23
    434908  758  777 N/A N/A TGTCACCTGGCAACCATTTT 49 24
    434909  778  797 10843 10862 GCACAAGCATAAAAGGTTCC 26 25
    434916  940  959 13493 13512 TGGGAGATCCGGCAGCCCTC 66 26
    434917 1004 1023 13557 13576 GCCATTGTCCTCTGGGTAGG 38 27
    434918 1042 1061 13595 13614 TCCAGGTGGCTCAGCAGCTT 25 28
    434919 1063 1082 13616 13635 ATCCAGAGGACCACGCCCCT 78 29
    434920 1068 1087 13621 13640 GGGCCATCCAGAGGACCACG 36 30
    434921 1119 1138 13672 13691 CGTCCCAGTAGATCCTGCTC 46 31
    434922 1187 1206 13740 13759 GTCAAAGAGCTTGCAGGTCT 32 32
    434923 1192 1211 13745 13764 TGTGTGTCAAAGAGCTTGCA 17 33
    434924 1344 1363 19461 19480 GTTGTCTGGCTAGCAGAGGT 33 34
    434925 1364 1383 19481 19500 TTGTTGAGCAAAATAATATA 97 35
    434926 1391 1410 19508 19527 GTAGCCCCTCAGGAAATGTC 15 36
    434927 1420 1439 19537 19556 TCTGGATTGCTGATGTGTTC 46 37
    434928 1430 1449 19547 19566 GTGGTAATCTTCTGGATTGC 42 38
    434929 1450 1469 19567 19586 GAGGAATGGCGGATAGATCT 63 39
    434930 1707 1726 19824 19843 CACTAAAGTCAAATATTTAC 88 40
    434931 1712 1731 19829 19848 GCTTTCACTAAAGTCAAATA 29 41
    434932 1821 1840 19938 19957 CAGATGTCACTGATTTTCCA 41 42
    434933 1826 1845 19943 19962 CCAATCAGATGTCACTGATT 44 43
    434934 1838 1857 19955 19974 TAAGCTCATCTGCCAATCAG 71 44
    434935 2196 2215 20313 20332 CCAAGGCTACAGGCACGGCT 29 45
    434936 2234 2253 20351 20370 ACACCAGGAAACCGCTGGCA 37 46
    434937 2293 2312 20410 20429 CTTCCAGGAAAGGCCAAGGA 23 47
    434938 2356 2375 20473 20492 TGTCCCATCCAAGAGTAGCG 30 48
    434939 2662 2681 20779 20798 CTTCCAGTGGTGGGTCCTGG 53 49
    434940 2705 2724 20822 20841 AACAGCCCACTGAGTGTGCA 43 50
    434941 2711 2730 20828 20847 AGCAGAAACAGCCCACTGAG 58 51
    434942 3435 3454 21552 21571 CTGGGTACATGGCAGTGGAG 27 52
    434943 3805 3824 21922 21941 GCATTTTCCAGAAAATTCAG 33 53
    434944 4477 4496 22594 22613 CCCAGAGTTGTTCCACCCCT 21 54
    434945 N/A N/A 22826 22845 GCTGGCCACAGAGGACTTCG 21 55
    434946 4737 4756 22854 22873 GCCTTCACGCACCATTCAGA 52 56
    434947 4812 4831 22929 22948 CCACCTGCATCGAGATCAGT 31 57
    434948 4818 4837 22935 22954 GGAGATCCACCTGCATCGAG 32 58
    434949 5035 5054 23152 23171 GGAAGTGGACCCCATTGCCT 17 59
    434952 N/A N/A 18834 18853 ATCTAAGGCAAGCTGAATGC 67 60
    434953 N/A N/A 18839 18858 ACAGCATCTAAGGCAAGCTG 38 61
    434954 N/A N/A 18845 18864 GAATTTACAGCATCTAAGGC 52 62
    434955 N/A N/A 18850 18869 TTCCTGAATTTACAGCATCT 21 63
    434957 N/A N/A  5359  5378 GCCGGAGACCTTGAAGAGCG 94 64
    434958 N/A N/A  7480  7499 ACTGGTCAGAATCTTGAAAA 94 65
    434959 N/A N/A  9101  9120 GTTGTGAACCTGCTAAAGGA 90 66
    434960 N/A N/A 10818 10837 CCTGGCAACCTGCATTTGCA 43 67
    434961 N/A N/A 10823 10842 TGTCACCTGGCAACCTGCAT 45 68
    434962 N/A N/A 12030 12049 GGGCAGGTTTCATTTCATTT 33 69
    434963 N/A N/A 13414 13433 GCCGGCAGTCTGCAAACACA 58 70
    434964 N/A N/A 19448 19467 CAGAGGTTCTACCTTTAATA 50 71
  • Example 2: Effect of 3-10-3 cEt Gapmers with Phosphorothioate Internucleoside Linkages on Human IRF4 In Vitro, Single Dose
  • Modified oligonucleotides complementary to a human IRF4 nucleic acid were designed and tested for their effect on IRF4 mRNA in vitro.
  • Cultured SK-MEL-28 cells at a density of 20,000 cells per well were transfected using electroporation with 4,000 nM concentration of modified oligonucleotide or no modified oligonucleotide for untreated controls. After approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by quantitative real-time PCR. Human primer probe set RTS3114 (described hereinabove in Example 1) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN®. Results are presented in the table below as percent control of the amount of IRF4 mRNA, relative to untreated control (UTC) cells.
  • The modified oligonucleotides in Tables 2 and 3 are 3-10-3 cEt gapmers. The gapmers are 16 nucleobases in length, wherein the central gap segment comprises ten 2′-deoxynucleosides and is flanked by wing segments on both the 5′ end and on the 3′ end comprising three cEt nucleosides. The sugar motif for the gapmers is (from 5′ to 3′): kkkddddddddddkkk; wherein ‘d’ represents a 2′-deoxyribose sugar and ‘k’ represents a cEt modified sugar. Each internucleoside linkage is a phosphorothioate internucleoside linkage and each cytosine residue is a 5-methylcytosine. “Start Site” indicates the 5′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence. “Stop Site” indicates the 3′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Each modified oligonucleotide listed in Tables 2 and 3 below is complementary to human IRF4 nucleic acid sequences SEQ ID NO: 1 or SEQ ID NO: 2, as indicated. ‘N/A’ indicates that the modified oligonucleotide is not complementary to that particular nucleic acid sequence with 100% complementarity. As shown below, modified oligonucleotides complementary to human IRF4 reduced the amount of human IRF4 mRNA.
  • TABLE 2
     Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ SEQ SEQ SEQ
    ID: 1 ID: 1 ID: 2 ID: 2 IRF4 SEQ
    Compound Start Stop Start Stop (% ID
    Number Site Site Site Site Sequence UTC) NO
    609281  156  171  5183  5198 GCTCATGCCGAACTCT  81  72
    609282  213  228  5240  5255 GCTGTCGATCTGGTCG  91  73
    609283  216  231  5243  5258 GCCGCTGTCGATCTGG  76  74
    609284  219  234  5246  5261 CTTGCCGCTGTCGATC  75  75
    609285  222  237  5249  5264 GTACTTGCCGCTGTCG  73  76
    609286  238  253  5265  5280 CCCACACCAGCCCGGG 106  77
    609287  241  256  5268  5283 TCTCCCACACCAGCCC  94  78
    609288  244  259  5271  5286 CGTTCTCCCACACCAG  52  79
    609289  294  309  5321  5336 GTCCTGCTTGCCCGCG  69  80
    609290  297  312  5324  5339 GTAGTCCTGCTTGCCC  56  81
    609291  334  349 N/A N/A CCCAAGCCTTGAAGAG  94  82
    609292  431  446  6910  6925 AAGTCATTGCTCTTGT  72  83
    609293  434  449  6913  6928 TCAAAGTCATTGCTCT  79  84
    609294  437  452  6916  6931 TCCTCAAAGTCATTGC  68  85
    609295  496  511  6975  6990 GAACAATCCTGTACAC 105  86
    609296  514  529  6993  7008 CTTTTTTGGCTCCCTC  64  87
    609297  517  532 N/A N/A CTCCTTTTTTGGCTCC  81  88
    609298  610  625 N/A N/A GAACCTGCTGGGCTGG  64  89
    609299  730  745  9220  9235 CTTGCCAGTGGTGGCC  84  90
    609300  733  748  9223  9238 GGCCTTGCCAGTGGTG 112  91
    609301  752  767 N/A N/A CAACCATTTTCACAAG  83  92
    609302  755  770 N/A N/A TGGCAACCATTTTCAC  93  93
    609303  758  773 N/A N/A ACCTGGCAACCATTTT  96  94
    609304  761  776 N/A N/A GTCACCTGGCAACCAT  59  95
    609305  764  779 10829 10844 CCTGTCACCTGGCAAC  59  96
    609306  767  782 10832 10847 GTTCCTGTCACCTGGC  51  97
    609307  770  785 10835 10850 AAGGTTCCTGTCACCT 102  98
    609308  773  788 10838 10853 TAAAAGGTTCCTGTCA  94  99
    609309  776  791 10841 10856 GCATAAAAGGTTCCTG  74 100
    609310  780  795 10845 10860 ACAAGCATAAAAGGTT  96 101
    609311  799  814 10864 10879 CCTGGGACTCAGGTGG  41 102
    609312  802  817 10867 10882 GAGCCTGGGACTCAGG  51 103
    609313  832  847 10897 10912 ACCTTATGCTTGGCTC  69 104
    609314  835  850 10900 10915 CAGACCTTATGCTTGG  90 105
    609317  943  958 13496 13511 GGGAGATCCGGCAGCC 110 106
    609318  979  994 13532 13547 CCTGGTCCAGGTTGCT  74 107
    609319  982  997 13535 13550 GGACCTGGTCCAGGTT 102 108
    609320  985 1000 13538 13553 ACAGGACCTGGTCCAG  65 109
    609321 1046 1061 13599 13614 TCCAGGTGGCTCAGCA  59 110
    609322 1049 1064 13602 13617 CTCTCCAGGTGGCTCA  87 111
    609323 1052 1067 13605 13620 CCCCTCTCCAGGTGGC  87 112
    609324 1194 1209 13747 13762 TGTGTCAAAGAGCTTG  78 113
    609325 1198 1213 13751 13766 GCTGTGTGTCAAAGAG  94 114
    609326 1201 1216 13754 13769 ACTGCTGTGTGTCAAA 106 115
    609327 1264 1279 17057 17072 GAGTCACCTGGAATCT  57 116
    609328 1291 1306 17084 17099 GGTCTGGAAACTCCTC  48 117
    609329 1294 1309 17087 17102 GAGGGTCTGGAAACTC 104 118
    609330 1297 1312 17090 17105 TCTGAGGGTCTGGAAA  91 119
    609331 1321 1336 17114 17129 GAGCTGTGATGAGCTT  90 120
    609332 1342 1357 19459 19474 TGGCTAGCAGAGGTTC  44 121
    609333 1345 1360 19462 19477 GTCTGGCTAGCAGAGG  34 122
    609334 1348 1363 19465 19480 GTTGTCTGGCTAGCAG  41 123
    609335 1389 1404 19506 19521 CCTCAGGAAATGTCCA  63 124
    609336 1393 1408 19510 19525 AGCCCCTCAGGAAATG  76 125
    609337 2068 2083 20185 20200 CTTCCCTGAGAAATGG  50 126
    609338 2071 2086 20188 20203 TTACTTCCCTGAGAAA  80 127
    609339 2719 2734 20836 20851 AATAAGCAGAAACAGC 101 128
    609340 3533 3548 21650 21665 ATCTATAAGATGTATA 101 129
    609341 3536 3551 21653 21668 TGCATCTATAAGATGT  68 130
    609342 3803 3818 21920 21935 TCCAGAAAATTCAGCT  52 131
    609343 3809 3824 21926 21941 GCATTTTCCAGAAAAT  36 132
    609344 N/A N/A  6995  7010 ACCTTTTTTGGCTCCC  79 133
    609345 N/A N/A  7740  7755 ATTCTTAGAATGCATA  62 134
    609346 N/A N/A  8504  8519 CAAACTCCTCAGGGAA  77 135
    609347 N/A N/A  9242  9257 TTACCATTTTCACAAG  92 136
    609348 N/A N/A 10796 10811 AATCAGATGATGTCTA 103 137
    609349 N/A N/A 10813 10828 CTGCATTTGCAAATAA 121 138
    609350 N/A N/A 10819 10834 GGCAACCTGCATTTGC 113 139
    609351 N/A N/A 10825 10840 TCACCTGGCAACCTGC  75 140
    609352 N/A N/A 11951 11966 CACCCACACAAGTCTT  91 141
    609353 N/A N/A 11972 11987 GTTTATTTCCTACTCT  84 142
    609354 N/A N/A 11978 11993 ATAGCTGTTTATTTCC  38 143
    609355 N/A N/A 11985 12000 GATATAAATAGCTGTT  63 144
    609356 N/A N/A 12024 12039 CATTTCATTTAATGTC  67 145
    609357 N/A N/A 12031 12046 CAGGTTTCATTTCATT  40 146
    609358 N/A N/A 13795 13810 CCTCCATTCTAACAGA 118 147
  • TABLE 3
     Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ SEQ SEQ SEQ
    ID: 1 ID: 1 ID: 2 ID: 2 IRF4 SEQ
    Compound Start Stop Start Stop (% ID
    Number Site Site Site Site Sequence UTC) NO
    609360 4711 4726 22828 22843 TGGCCACAGAGGACTT  67 148
    609361    1   16  3740  3755 ACTGAGAGTGCGAGGT 120 149
    609362  121  136  5148  5163 CCAGGTTCATGCCCCG  46 150
    609363  181  196  5208  5223 GCTTCCCGTTGCCGCA  82 151
    609364  300   315  5327  5342 GTTGTAGTCCTGCTTG  78 152
    609365  420  435  6899  6914 CTTGTTCAAAGCGCAC  68 153
    609366  480  495  6959  6974 TTTGTACGGGTCTGAG  80 154
    609367  672  687  9162  9177 GTGTGGCTGATCCGGG  73 155
    609368  736  751  9226  9241 CTGGGCCTTGCCAGTG 114 156
    609369  810  825 10875 10890 GACTCCGGGAGCCTGG  35 157
    609371 1004 1019 13557 13572 TTGTCCTCTGGGTAGG  70 158
    609372 1124 1139 13677 13692 CCGTCCCAGTAGATCC  75 159
    609373 1184 1199 13737 13752 AGCTTGCAGGTCTGGT  47 160
    609374 1431 1446 19548 19563 GTAATCTTCTGGATTG  71 161
    609375 1527 1542 19644 19659 TCCCCGTATCAAAAAA 112 162
    609376 1682 1697 19799 19814 CACTTGTCTTGGGTGG  55 163
    609377 1742 1757 19859 19874 AACAGTAAGAGGGCAG  37 164
    609378 1866 1881 19983 19998 GCAAAGCCACCCTTCC  40 165
    609379 1986 2001 20103 20118 TCTTCCAGCAAGACCT  72 166
    609380 2111 2126 20228 20243 ATACATTTCTTTTACG  78 167
    609381 2171 2186 20288 20303 GATTCATTTCCTTCAC  51 168
    609382 2231 2246 20348 20363 GAAACCGCTGGCAGGT  50 169
    609383 2295 2310 20412 20427 TCCAGGAAAGGCCAAG  51 170
    609384 2304 2319 20421 20436 TAACTGGCTTCCAGGA  70 171
    609385 2365 2380 20482 20497 AAAAATGTCCCATCCA  70 172
    609386 2431 2446 20548 20563 GTCAAAAAGATGCAGA  50 173
    609387 2494 2509 20611 20626 GATTTATGTTCCTTAA  53 174
    609388 2574 2589 20691 20706 AACAAACAGAGGAGCG  84 175
    609389 2634 2649 20751 20766 GCCTGGGAGTCCCCGG  82 176
    609390 2694 2709 20811 20826 GTGCAGTTCCGTAGTC  79 177
    609391 2754 2769 20871 20886 ACTATAATTGGCACGA  31 178
    609392 2816 2831 20933 20948 TCTTTGGGATTCTATA  40 179
    609393 2936 2951 21053 21068 GGAGTAATAGTAAATA  64 180
    609394 3081 3096 21198 21213 CTGCTCACTAAGCTTG  27 181
    609395 3147 3162 21264 21279 GTATTAATATTCTGAC  37 182
    609396 3216 3231 21333 21348 GGAGATCCTTTTTATT  68 183
    609397 3336 3351 21453 21468 GACTCCATGAGGTTTT  30 184
    609398 3437 3452 21554 21569 GGGTACATGGCAGTGG  32 185
    609399 3591 3606 21708 21723 GCAGTTCTTAATATCA  40 186
    609400 3657 3672 21774 21789 TGAAGTGCTGTGTGGG  43 187
    609401 3717 3732 21834 21849 TCCGCTTGGAGAATTA  87 188
    609402 3782 3797 21899 21914 GTTAAAGCAGCATAAT  73 189
    609403 3851 3866 21968 21983 AGATGTAAAGATAGGA  46 190
    609404 3911 3926 22028 22043 AGTTCATTCCCTAGGT  56 191
    609405 3971 3986 22088 22103 GTTCCTTTTCAGAGTC  28 192
    609406 4031 4046 22148 22163 AGTACAAACTAAATTC  76 193
    609407 4166 4181 22283 22298 GAGGTTTTCCTAAATA  31 194
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT  21 195
    609409 4359 4374 22476 22491 CTGTAGGATTTTACAT  76 196
    609410 4479 4494 22596 22611 CAGAGTTGTTCCACCC  38 197
    609411 4599 4614 22716 22731 AATGAACGGAAGTTTA  67 198
    609412 4665 4680 22782 22797 AACCAATCCCAACACT  88 199
    609413 4727 4742 22844 22859 TTCAGACAGATGCAGC  38 200
    609414 4800 4815 22917 22932 CAGTCTCAAAAACGGG  49 201
    609415 4862 4877 22979 22994 ACCTTTACTTCATTCC  36 202
    609416 4987 5002 23104 23119 ACGGGAATTTCCATTG  33 203
    609417 5037 5052 23154 23169 AAGTGGACCCCATTGC  69 204
    609418 5077 5092 23194 23209 TTCAGCAGAAAGTGGG  52 205
    609419 5146 5161 23263 23278 CGCAGAGCCAGTAGGG  33 206
    609420 N/A N/A  2604  2619 AAAAGCCCAAAATAGG 112 207
     2875  2890
    609421 N/A N/A  8538  8553 CTGGCATTGAGACGGG 39  208
     8746  8761
     8850  8865
     8902  8917
     9058  9073
    609422 N/A N/A  8542  8557 AGCACTGGCATTGAGA  26 209
     8750  8765
     8854  8869
     8906  8921
     9062  9077
    609423 N/A N/A  8547  8562 TAAGAAGCACTGGCAT  74 210
     8703  8718
     8807  8822
     8963  8978
     9067  9082
    609424 N/A N/A  8552  8567 TGAGATAAGAAGCACT  80 211
     8708  8723
     8812  8827
     8968  8983
     9072  9087
    609425 N/A N/A  8560  8575 GGAGAGGCTGAGATAA   71 212
     8716  8731
     8820  8835
     8976  8991
     9080  9095
    609426 N/A N/A  8561  8576 AGGAGAGGCTGAGATA  79 213
     8613  8628
     8665  8680
     8717  8732
     8769  8784
     8821  8836
     8873  8888
     8925  8940
     8977  8992
     9029  9044
     9081  9096
    609427 N/A N/A  8565  8580 GTGCAGGAGAGGCTGA  68 214
     8617  8632
     8669  8684
     8721  8736
     8773  8788
     8825  8840
     8877  8892
     8929  8944
     8981  8996
     9033  9048
     9085  9100
    609428 N/A N/A  8567  8582 GAGTGCAGGAGAGGCT  69 215
     8619  8634
     8671  8686
     8723  8738
     8775  8790
     8827  8842
     8879  8894
     8931  8946
     8983  8998
     9035  9050
     9087  9102
    609429 N/A N/A  8568  8583 GGAGTGCAGGAGAGGC  84 216
     8620  8635
     8672  8687
     8724  8739
     8776  8791
     8828  8843
     8880  8895
     8932  8947
     8984  8999
     9036  9051
     9088  9103
    609430 N/A N/A  8572  8587 TAAAGGAGTGCAGGAG 107 217
     8624  8639
     8676  8691
     8728  8743
     8780  8795
     8832  8847
     8884  8899
     8936  8951
     8988  9003
     9040  9055
     9092  9107
    609431 N/A N/A  8573  8588 GTAAAGGAGTGCAGGA  91 218
     8625  8640
     8677  8692
     8729  8744
     8833  8848
     8885  8900
     8937  8952
     8989  9004
     9041  9056
    609432 N/A N/A  8575  8590 GGGTAAAGGAGTGCAG  81 219
     8627  8642
     8679  8694
     8731  8746
     8835  8850
     8887  8902
     8939  8954
     8991  9006
     9043  9058
    609433 N/A N/A  8590  8605 CTGGCATCGAGACGGG  53 220
     8642  8657
     8694  8709
     8798  8813
     8954  8969
     9006  9021
    609434 N/A N/A  8593  8608 GCACTGGCATCGAGAC  43 221
     8645  8660
     8697  8712
     8801  8816
     8957  8972
     9009  9024
    609435 N/A N/A  8596  8611 GAAGCACTGGCATCGA  56 222
     8648  8663
     8700  8715
     8804  8819
     8960  8975
     9012  9027
    609436 N/A N/A 18852 18867 CCTGAATTTACAGCAT  60 223
  • Example 3: Effect of 4-8-4 cEt Gapmers with Phosphorothioate Internucleoside Linkages on Human IRF4 In Vitro, Single Dose
  • Modified oligonucleotides complementary to a human IRF4 nucleic acid were designed and tested for their effect on IRF4 mRNA in vitro.
  • Cultured SK-MEL-28 cells at a density of 20,000 cells per well were transfected using electroporation with 4,000 nM concentration of modified oligonucleotide or no modified oligonucleotide for untreated controls. After approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by quantitative real-time PCR. Human primer probe set RTS3114 (described hereinabove in Example 1) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN®. Results are presented in the table below as percent control of the amount of IRF4 mRNA, relative to untreated control (UTC) cells.
  • The modified oligonucleotides in Table 4 are 4-8-4 cEt gapmers. The gapmers are 16 nucleobases in length, wherein the central gap segment comprises eight 2′-deoxynucleosides and is flanked by wing segments on both the 5′ end and on the 3′ end comprising four cEt nucleosides. The sugar motif for the gapmers is (from 5′ to 3′): kkkkddddddddkkkk; wherein ‘d’ represents a 2′-deoxyribose sugar and ‘k’ represents a cEt modified sugar. Each internucleoside linkage is a phosphorothioate internucleoside linkage and each cytosine residue is a 5-methylcytosine. “Start Site” indicates the 5′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence. “Stop Site” indicates the 3′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Each modified oligonucleotide listed in Table 4 below is complementary to human IRF4 nucleic acid sequences SEQ ID NO: 1 or SEQ ID NO: 2, as indicated. ‘N/A’ indicates that the modified oligonucleotide is not complementary to that particular nucleic acid sequence with 100% complementarity. As shown below, modified oligonucleotides complementary to human IRF4 reduced the amount of human IRF4 mRNA.
  • TABLE 4
    Percent control of human IRF4 mRNA with 4-8-4 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2 SEQ
    Compound Start Stop Start Stop IRF4 ID
    Number Site Site Site Site Sequence (% UTC) NO
    609518 156 171 5183 5198 GCTCATGCCGAACTCT 70 72
    609519 213 228 5240 5255 GCTGTCGATCTGGTCG 94 73
    609520 216 231 5243 5258 GCCGCTGTCGATCTGG 85 74
    609521 219 234 5246 5261 CTTGCCGCTGTCGATC 58 75
    609522 222 237 5249 5264 GTACTTGCCGCTGTCG 64 76
    609523 238 253 5265 5280 CCCACACCAGCCCGGG 106 77
    609524 241 256 5268 5283 TCTCCCACACCAGCCC 75 78
    609525 244 259 5271 5286 CGTTCTCCCACACCAG 101 79
    609526 294 309 5321 5336 GTCCTGCTTGCCCGCG 86 80
    609527 297 312 5324 5339 GTAGTCCTGCTTGCCC 89 81
    609528 334 349 N/A N/A CCCAAGCCTTGAAGAG 78 82
    609529 431 446 6910 6925 AAGTCATTGCTCTTGT 72 83
    609530 434 449 6913 6928 TCAAAGTCATTGCTCT 43 84
    609531 437 452 6916 6931 TCCTCAAAGTCATTGC 90 85
    609532 496 511 6975 6990 GAACAATCCTGTACAC 100 86
    609533 514 529 6993 7008 CTTTTTTGGCTCCCTC 54 87
    609534 517 532 N/A N/A CTCCTTTTTTGGCTCC 93 88
    609535 610 625 N/A N/A GAACCTGCTGGGCTGG 87 89
    609536 730 745 9220 9235 CTTGCCAGTGGTGGCC 109 90
    609537 733 748 9223 9238 GGCCTTGCCAGTGGTG 94 91
    609538 752 767 N/A N/A CAACCATTTTCACAAG 95 92
    609539 755 770 N/A N/A TGGCAACCATTTTCAC 93 93
    609540 758 773 N/A N/A ACCTGGCAACCATTTT 81 94
    609541 761 776 N/A N/A GTCACCTGGCAACCAT 59 95
    609542 764 779 10829 10844 CCTGTCACCTGGCAAC 63 96
    609543 767 782 10832 10847 GTTCCTGTCACCTGGC 88 97
    609544 770 785 10835 10850 AAGGTTCCTGTCACCT 86 98
    609545 773 788 10838 10853 TAAAAGGTTCCTGTCA 57 99
    609546 776 791 10841 10856 GCATAAAAGGTTCCTG 53 100
    609547 780 795 10845 10860 ACAAGCATAAAAGGTT 60 101
    609548 799 814 10864 10879 CCTGGGACTCAGGTGG 93 102
    609549 802 817 10867 10882 GAGCCTGGGACTCAGG 81 103
    609550 832 847 10897 10912 ACCTTATGCTTGGCTC 70 104
    609551 835 850 10900 10915 CAGACCTTATGCTTGG 74 105
    609554 943 958 13496 13511 GGGAGATCCGGCAGCC 113 106
    609555 979 994 13532 13547 CCTGGTCCAGGTTGCT 66 107
    609556 982 997 13535 13550 GGACCTGGTCCAGGTT 128 108
    609557 985 1000 13538 13553 ACAGGACCTGGTCCAG 93 109
    609558 1046 1061 13599 13614 TCCAGGTGGCTCAGCA 66 110
    609559 1049 1064 13602 13617 CTCTCCAGGTGGCTCA 88 111
    609560 1052 1067 13605 13620 CCCCTCTCCAGGTGGC 101 112
    609561 1194 1209 13747 13762 TGTGTCAAAGAGCTTG 74 113
    609562 1198 1213 13751 13766 GCTGTGTGTCAAAGAG 60 114
    609563 1201 1216 13754 13769 ACTGCTGTGTGTCAAA 81 115
    609564 1264 1279 17057 17072 GAGTCACCTGGAATCT 94 116
    609565 1291 1306 17084 17099 GGTCTGGAAACTCCTC 69 117
    609566 1294 1309 17087 17102 GAGGGTCTGGAAACTC 92 118
    609567 1297 1312 17090 17105 TCTGAGGGTCTGGAAA 97 119
    609568 1321 1336 17114 17129 GAGCTGTGATGAGCTT 95 120
    609569 1342 1357 19459 19474 TGGCTAGCAGAGGTTC 91 121
    609570 1345 1360 19462 19477 GTCTGGCTAGCAGAGG 91 122
    609571 1348 1363 19465 19480 GTTGTCTGGCTAGCAG 48 123
    609572 1389 1404 19506 19521 CCTCAGGAAATGTCCA 90 124
    609574 2068 2083 20185 20200 CTTCCCTGAGAAATGG 64 126
    609575 2071 2086 20188 20203 TTACTTCCCTGAGAAA 86 127
    609576 2719 2734 20836 20851 AATAAGCAGAAACAGC 61 128
    609577 3533 3548 21650 21665 ATCTATAAGATGTATA 64 129
    609578 3536 3551 21653 21668 TGCATCTATAAGATGT 90 130
    609579 3803 3818 21920 21935 TCCAGAAAATTCAGCT 74 131
    609580 3809 3824 21926 21941 GCATTTTCCAGAAAAT 63 132
    609581 N/A N/A 6995 7010 ACCTTTTTTGGCTCCC 81 133
    609582 N/A N/A 7740 7755 ATTCTTAGAATGCATA 67 134
    609583 N/A N/A 8504 8519 CAAACTCCTCAGGGAA 83 135
    609584 N/A N/A 9242 9257 TTACCATTTTCACAAG 93 136
    609585 N/A N/A 10796 10811 AATCAGATGATGTCTA 113 137
    609586 N/A N/A 10813 10828 CTGCATTTGCAAATAA 108 138
    609587 N/A N/A 10819 10834 GGCAACCTGCATTTGC 112 139
    609588 N/A N/A 10825 10840 TCACCTGGCAACCTGC 72 140
    609589 N/A N/A 11951 11966 CACCCACACAAGTCTT 86 141
    609590 N/A N/A 11972 11987 GTTTATTTCCTACTCT 56 142
    609591 N/A N/A 11978 11993 ATAGCTGTTTATTTCC 41 143
    609592 N/A N/A 11985 12000 GATATAAATAGCTGTT 39 144
    609593 N/A N/A 12024 12039 CATTTCATTTAATGTC 56 145
    609594 N/A N/A 12031 12046 CAGGTTTCATTTCATT 46 146
    609595 N/A N/A 13795 13810 CCTCCATTCTAACAGA 122 147
  • Example 4: Effect of 3-10-3 cEt Gapmers with Phosphorothioate Internucleoside Linkages on Human IRF4 In Vitro, Single Dose
  • Modified oligonucleotides complementary to a human IRF4 nucleic acid were designed and tested for their effect on IRF4 mRNA in vitro.
  • Cultured SK-MEL-28 cells at a density of 20,000 cells per well were transfected using electroporation with 4,000 nM concentration of modified oligonucleotide or no modified oligonucleotide for untreated controls. After approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by quantitative real-time PCR. Human primer probe set RTS3114 (described hereinabove in Example 1) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN®. Results are presented in the table below as percent control of the amount of IRF4 mRNA, relative to untreated control (UTC) cells.
  • The modified oligonucleotides in Tables 5 through 12 are 3-10-3 cEt gapmers. The gapmers are 16 nucleobases in length, wherein the central gap segment comprises ten 2′-deoxynucleosides and is flanked by wing segments on both the 5′ end and on the 3′ end comprising three cEt nucleosides. The sugar motif for the gapmers is (from 5′ to 3′): kkkddddddddddkkk; wherein ‘d’ represents a 2′-deoxyribose sugar and ‘k’ represents a cEt modified sugar. Each internucleoside linkage is a phosphorothioate internucleoside linkage and each cytosine residue is a 5-methylcytosine. “Start Site” indicates the 5′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence. “Stop Site” indicates the 3′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Each modified oligonucleotide listed in Tables 5 through 12 below is complementary to human IRF4 nucleic acid sequences SEQ ID NO: 1 or SEQ ID NO: 2, as indicated. ‘N/A’ indicates that the modified oligonucleotide is not complementary to that particular nucleic acid sequence with 100% complementarity. As shown below, modified oligonucleotides complementary to human IRF4 reduced the amount of human IRF4 mRNA.
  • TABLE 5
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence (% UTC) ID NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 24 195
    666225 5 20 3744 3759 TGAAACTGAGAGTGCG 81 224
    666226 12 27 3751 3766 CGAGCGGTGAAACTGA 67 225
    666227 19 34 3758 3773 CCAAGATCGAGCGGTG 63 226
    666228 26 41 3765 3780 GTGGGTCCCAAGATCG 60 227
    666229 40 55 3779 3794 AGCTGAGGGCAGCGGT 107 228
    666230 47 62 3786 3801 GACTCGGAGCTGAGGG 77 229
    666231 54 69 3793 3808 CGCCCTGGACTCGGAG 64 230
    666232 61 76 N/A N/A CTGCACTCGCCCTGGA 58 231
    666233 68 83 N/A N/A CTCTGCTCTGCACTCG 59 232
    666234 75 90 5102 5117 CCGCCCGCTCTGCTCT 46 233
    666235 82 97 5109 5124 GGGTCCTCCGCCCGCT 72 234
    666236 101 116 5128 5143 CCGTCCGCGCCCGCGC 39 235
    666237 129 144 5156 5171 GCCGCCCTCCAGGTTC 51 236
    666238 136 151 5163 5178 CTCGGCCGCCGCCCTC 63 237
    666239 143 158 5170 5185 TCTCCGCCTCGGCCGC 59 238
    666240 150 165 5177 5192 GCCGAACTCTCCGCCT 49 239
    666241 160 175 5187 5202 CCGCGCTCATGCCGAA 55 240
    666242 167 182 5194 5209 CAGCTCACCGCGCTCA 58 241
    666243 185 200 5212 5227 CGGAGCTTCCCGTTGC 65 242
    666244 192 207 5219 5234 CCACTGGCGGAGCTTC 64 243
    666245 304 319 5331 5346 CGCGGTTGTAGTCCTG 56 244
    666246 311 326 5338 5353 TCCTCCTCGCGGTTGT 41 245
    666247 327 342 5354 5369 CTTGAAGAGCGCGGCG 79 246
    666248 338 353 N/A N/A AGTGCCCAAGCCTTGA 52 247
    666249 348 363 6827 6842 TCCTTTAAACAGTGCC 50 248
    666250 356 371 6835 6850 CGGAACTTTCCTTTAA 63 249
    666251 363 378 6842 6857 GCCTTCTCGGAACTTT 68 250
    666252 370 385 6849 6864 TGTCGATGCCTTCTCG 72 251
    666253 377 392 6856 6871 TCCGGCTTGTCGATGC 59 252
    666254 396 411 6875 6890 CGTCTTCCAGGTGGGA 84 253
    666256 425 440 6904 6919 TTGCTCTTGTTCAAAG 71 254
    666257 449 464 6928 6943 CGCTCAACCAGTTCCT 72 255
    666258 456 471 6935 6950 CTGGCTCCGCTCAACC 48 256
    666259 463 478 6942 6957 TGTCCAGCTGGCTCCG 61 257
    666260 470 485 6949 6964 TCTGAGATGTCCAGCT 55 258
    666261 484 499 6963 6978 ACACTTTGTACGGGTC 44 259
    666262 507 522 6986 7001 GGCTCCCTCAGGAACA 81 260
    666263 521 536 N/A N/A TTGGCTCCTTTTTTGG 87 261
    666264 528 543 7846 7861 GAGCTGCTTGGCTCCT 81 262
    666265 535 550 7853 7868 CCAGGGTGAGCTGCTT 69 263
    666266 546 561 7864 7879 CTGCGGGTCCTCCAGG 80 264
    666267 553 568 7871 7886 TGGACATCTGCGGGTC 56 265
    666268 560 575 7878 7893 TGGCTCATGGACATCT 68 266
    666269 577 592 7895 7910 TTGTCATGGTGTAGGG 59 267
    666270 593 608 7911 7926 AGCGAAGGGTAAGGCG 86 268
    666271 621 636 9111 9126 CATGTAGTTGTGAACC 73 269
    666272 628 643 9118 9133 GTGGCATCATGTAGTT 73 270
    666273 644 659 9134 9149 CAGCTTCGGTCGAGGG 42 271
    666274 651 666 9141 9156 GTCCCTCCAGCTTCGG 97 272
    666275 676 691 9166 9181 CCGGGTGTGGCTGATC 84 273
    666276 695 710 9185 9200 GGACATTGGTACGGGA 50 274
    666277 702 717 9192 9207 CGTCATGGGACATTGG 44 275
    666278 725 740 9215 9230 CAGTGGTGGCCGCGGG 73 276
    666279 740 755 9230 9245 CAAGCTGGGCCTTGCC 66 277
    666280 747 762 9237 9252 ATTTTCACAAGCTGGG 61 278
    666281 771 786 10836 10851 AAAGGTTCCTGTCACC 62 279
    666282 775 790 10840 10855 CATAAAAGGTTCCTGT 91 280
    666283 777 792 10842 10857 AGCATAAAAGGTTCCT 55 281
    666284 779 794 10844 10859 CAAGCATAAAAGGTTC 71 282
    666285 781 796 10846 10861 CACAAGCATAAAAGGT 74 283
    666286 784 799 10849 10864 GGGCACAAGCATAAAA 80 284
    666287 827 842 10892 10907 ATGCTTGGCTCTGTGG 24 285
    666294 947 962 13500 13515 CCATGGGAGATCCGGC 46 286
    666295 954 969 13507 13522 CGTATGTCCATGGGAG 12 287
    666296 975 990 13528 13543 GTCCAGGTTGCTGGCG 47 288
    666297 989 1004 13542 13557 GGGAACAGGACCTGGT 45 289
    666298 1008 1023 13561 13576 GCCATTGTCCTCTGGG 75 290
    666299 1015 1030 13568 13583 TCCTCTGGCCATTGTC 59 291
    666300 1033 1048 13586 13601 GCAGCTTCTCAATGTT 57 292
    666301 1042 1057 13595 13610 GGTGGCTCAGCAGCTT 63 293
  • TABLE 6
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence (% UTC) ID NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 23 195
    666302 1058 1073 13611 13626 ACCACGCCCCTCTCCA 91 294
    666303 1065 1080 13618 13633 CCAGAGGACCACGCCC 72 295
    666306 1101 1116 13654 13669 GCACAGTCTTTTCGCA 80 296
    666307 1109 1124 13662 13677 CTGCTCTGGCACAGTC 17 297
    666308 1116 1131 13669 13684 GTAGATCCTGCTCTGG 55 298
    666309 1128 1143 13681 13696 GGGCCCGTCCCAGTAG 80 299
    666311 1167 1182 13720 13735 TCTCTCCAGTTTGTTG 86 300
    666312 1188 1203 13741 13756 AAAGAGCTTGCAGGTC 63 301
    666313 1205 1220 13758 13773 AAGAACTGCTGTGTGT 88 302
    666314 1212 1227 N/A N/A CTCTGACAAGAACTGC 70 303
    666315 1219 1234 N/A N/A CTTGCAGCTCTGACAA 91 304
    666317 1241 1256 17034 17049 GAGCGGCCGTGGTGAG 59 305
    666318 1248 1263 17041 17056 TGGCAGGGAGCGGCCG 89 306
    666319 1255 1270 17048 17063 GGAATCTTGGCAGGGA 52 307
    666321 1275 1290 17068 17083 TCCAAAGCATAGAGTC 47 308
    666322 1287 1302 17080 17095 TGGAAACTCCTCTCCA 84 309
    666323 1311 1326 17104 17119 GAGCTTTCTTTGCCTC 87 310
    666324 1338 1353 N/A N/A TAGCAGAGGTTCTACG 76 311
    666326 1347 1362 19464 19479 TTGTCTGGCTAGCAGA 55 312
    666327 1349 1364 19466 19481 AGTTGTCTGGCTAGCA 20 313
    666328 1351 1366 19468 19483 ATAGTTGTCTGGCTAG 48 314
    666329 1353 1368 19470 19485 ATATAGTTGTCTGGCT 59 315
    666331 1381 1396 19498 19513 AATGTCCACTGTTTTG 53 316
    666333 1417 1432 19534 19549 TGCTGATGTGTTCTGG 33 317
    666335 1442 1457 19559 19574 ATAGATCTGTGGTAAT 62 318
    666336 1449 1464 19566 19581 ATGGCGGATAGATCTG 43 319
    666337 1456 1471 19573 19588 TAGAGGAATGGCGGAT 55 320
    666338 1463 1478 19580 19595 TCTTGAATAGAGGAAT 58 321
    666339 1485 1500 19602 19617 CACTCATCTTGACATT 64 322
    666341 1538 1553 19655 19670 AAGACCCCGTATCCCC 58 323
    666342 1686 1701 19803 19818 AAATCACTTGTCTTGG 51 324
    666343 1715 1730 19832 19847 CTTTCACTAAAGTCAA 49 325
    666344 1730 1745 19847 19862 GCAGTCAATTGGACGC 23 326
    666345 1737 1752 19854 19869 TAAGAGGGCAGTCAAT 83 327
    666346 1762 1777 19879 19894 TCCACTTCTGAATTCC 81 328
    666347 1775 1790 19892 19907 CTGAACTGAAATCTCC 36 329
    666348 1782 1797 19899 19914 TCAACCGCTGAACTGA 65 330
    666349 1789 1804 19906 19921 ATTCTCCTCAACCGCT 65 331
    666351 1803 1818 19920 19935 CTTGTCTCGCCGCAAT 35 332
    666352 1810 1825 19927 19942 TTCCATGCTTGTCTCG 38 333
    666353 1826 1841 19943 19958 TCAGATGTCACTGATT 65 334
    666354 1840 1855 19957 19972 AGCTCATCTGCCAATC 67 335
    666355 1848 1863 19965 19980 TTGAAATAAGCTCATC 67 336
    666356 1885 1900 20002 20017 TCTACAGAACACAAGA 108 337
    666357 1892 1907 20009 20024 ATGGCAGTCTACAGAA 102 338
    666358 1899 1914 20016 20031 ATCAATGATGGCAGTC 43 339
    666359 1908 1923 20025 20040 ACAGTGATCATCAATG 44 340
    666360 1915 1930 20032 20047 AATTTTCACAGTGATC 66 341
    666361 1922 1937 20039 20054 CTTGGTCAATTTTCAC 47 342
    666362 1929 1944 20046 20061 CACATCACTTGGTCAA 28 343
    666363 1956 1971 20073 20088 TAAAGAGCGCATTTCA 59 344
    666364 1963 1978 20080 20095 AACAAATTAAAGAGCG 77 345
    666365 1972 1987 20089 20104 CTAATCTACAACAAAT 77 346
    666366 2000 2015 20117 20132 GCAAGTTTTCTCTGTC 44 347
    666368 2023 2038 20140 20155 CTAGTCAGTGTCAATA 49 348
    666369 2030 2045 20147 20162 CATCACTCTAGTCAGT 41 349
    666370 2037 2052 20154 20169 AAGCAGTCATCACTCT 62 350
    666371 2053 2068 20170 20185 GCACAGACATACCTAC 54 351
    666373 2082 2097 20199 20214 CAATTTACATCTTACT 79 352
    666374 2089 2104 20206 20221 GCTTCTTCAATTTACA 55 353
    666375 2130 2145 20247 20262 GCAGCTCCTACATACA 47 354
    666376 2138 2153 20255 20270 CAAGAACTGCAGCTCC 53 355
    666377 2146 2161 20263 20278 GTCTTCCACAAGAACT 53 356
    666378 2153 2168 20270 20285 AGCAAGTGTCTTCCAC 25 357
  • TABLE 7
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence (% UTC) ID NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 23 195
    666379 2161 2176 20278 20293 CTTCACTCAGCAAGTG 57 358
    666380 2179 2194 20296 20311 CAGTCAAAGATTCATT 60 359
    666381 2193 2208 20310 20325 TACAGGCACGGCTTCA 42 360
    666382 2200 2215 20317 20332 CCAAGGCTACAGGCAC 37 361
    666383 2207 2222 20324 20339 GGCCTCCCCAAGGCTA 82 362
    666384 2235 2250 20352 20367 CCAGGAAACCGCTGGC 62 363
    666385 2243 2258 20360 20375 GACCCACACCAGGAAA 98 364
    666386 2250 2265 20367 20382 GCAGAGGGACCCACAC 79 365
    666387 2308 2323 20425 20440 TTACTAACTGGCTTCC 51 366
    666388 2315 2330 20432 20447 AGGAAGTTTACTAACT 42 367
    666389 2328 2343 20445 20460 GACTCAAGAAAATAGG 36 368
    666390 2335 2350 20452 20467 GTTTTTTGACTCAAGA 33 369
    666392 2355 2370 20472 20487 CATCCAAGAGTAGCGC 27 370
    666393 2376 2391 20493 20508 GTAGGACAGACAAAAA 77 371
    666394 2383 2398 20500 20515 CTAGATTGTAGGACAG 52 372
    666395 2390 2405 20507 20522 GACATTACTAGATTGT 30 373
    666396 2397 2412 20514 20529 TTACTTAGACATTACT 52 374
    666397 2404 2419 20521 20536 TTAACCATTACTTAGA 55 375
    666398 2435 2450 20552 20567 GAGGGTCAAAAAGATG 67 376
    666399 2450 2465 20567 20582 GCATCTCTAAAGAATG 39 377
    666400 2461 2476 20578 20593 GAAGAATTTTAGCATC 44 378
    666401 2468 2483 20585 20600 TTTATGCGAAGAATTT 67 379
    666402 2475 2490 20592 20607 CTTCTTCTTTATGCGA 34 380
    666403 2498 2513 20615 20630 TTAAGATTTATGTTCC 36 381
    666404 2514 2529 20631 20646 GGCAACAGTTCAAGTA 43 382
    666405 2521 2536 20638 20653 ACAGAAGGGCAACAGT 57 383
    666406 2528 2543 20645 20660 TACTTGGACAGAAGGG 38 384
    666407 2535 2550 20652 20667 AGTTAAGTACTTGGAC 58 385
    666408 2542 2557 20659 20674 AACAGATAGTTAAGTA 81 386
    666409 2578 2593 20695 20710 GCCAAACAAACAGAGG 78 387
    666410 2585 2600 20702 20717 CTGGACAGCCAAACAA 79 388
    666411 2592 2607 20709 20724 CTGATCGCTGGACAGC 80 389
    666412 2599 2614 20716 20731 GCCATGGCTGATCGCT 70 390
    666413 2606 2621 20723 20738 TAGTGTCGCCATGGCT 31 391
    666414 2613 2628 20730 20745 CCTCCTTTAGTGTCGC 35 392
    666415 2621 2636 20738 20753 CGGCTCCTCCTCCTTT 89 393
    666416 2628 2643 20745 20760 GAGTCCCCGGCTCCTC 75 394
    666417 2652 2667 20769 20784 TCCTGGCAGTGCTCTC 40 395
    666418 2659 2674 20776 20791 TGGTGGGTCCTGGCAG 77 396
    666420 2673 2688 20790 20805 CATCCTGCTTCCAGTG 70 397
    666421 2681 2696 20798 20813 GTCAGCTCCATCCTGC 48 398
    666422 2688 2703 20805 20820 TTCCGTAGTCAGCTCC 32 399
    666423 2698 2713 20815 20830 GAGTGTGCAGTTCCGT 33 400
    666424 2705 2720 20822 20837 GCCCACTGAGTGTGCA 90 401
    666425 2714 2729 20831 20846 GCAGAAACAGCCCACT 59 402
    666426 2737 2752 20854 20869 GAAGCATAGAACAGAT 49 403
    666427 2744 2759 20861 20876 GCACGAGGAAGCATAG 42 404
    666428 2749 2764 20866 20881 AATTGGCACGAGGAAG 72 405
    666429 2751 2766 20868 20883 ATAATTGGCACGAGGA 33 406
    666430 2753 2768 20870 20885 CTATAATTGGCACGAG 37 407
    666431 2755 2770 20872 20887 AACTATAATTGGCACG 27 408
    666432 2757 2772 20874 20889 CAAACTATAATTGGCA 47 409
    666433 2759 2774 20876 20891 GTCAAACTATAATTGG 39 410
    666434 2765 2780 20882 20897 GGCCCTGTCAAACTAT 60 411
    666435 2772 2787 20889 20904 ATTTTAAGGCCCTGTC 66 412
    666436 2779 2794 20896 20911 CCAAGTAATTTTAAGG 66 413
    666437 2793 2808 20910 20925 GCATTTGGAAAAAGCC 29 414
    666438 2810 2825 20927 20942 GGATTCTATAAATAGA 75 415
    666439 2820 2835 20937 20952 GAGGTCTTTGGGATTC 26 416
    666440 2827 2842 20944 20959 GCAAGTGGAGGTCTTT 26 417
    666441 2834 2849 20951 20966 TACTTAAGCAAGTGGA 25 418
    666442 2841 2856 20958 20973 ATAGGTATACTTAAGC 20 419
    666443 2848 2863 20965 20980 GTAAGTGATAGGTATA 24 420
    666444 2872 2887 20989 21004 GTACTTTCTCAAAACC 30 421
    666445 2879 2894 20996 21011 TACTGCTGTACTTTCT 57 422
    666446 2886 2901 21003 21018 CCCAGTCTACTGCTGT 34 423
    666447 2902 2917 21019 21034 GGCCTGGAGGTGACGC 59 424
    666448 2909 2924 21026 21041 GAGAAACGGCCTGGAG 56 425
    666449 2916 2931 21033 21048 GTAGTATGAGAAACGG 17 426
    666450 2923 2938 21040 21055 ATATCCTGTAGTATGA 43 427
    666451 2930 2945 21047 21062 ATAGTAAATATCCTGT 64 428
    666452 2940 2955 21057 21072 CCTGGGAGTAATAGTA 47 429
    666453 2947 2962 21064 21079 TGCTGATCCTGGGAGT 21 430
    666454 2954 2969 21071 21086 AATCTTCTGCTGATCC 28 431
    666455 2961 2976 21078 21093 GCTACGCAATCTTCTG 42 432
  • TABLE 8
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence (% UTC) ID NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 20 195
    666457 2975 2990 21092 21107 ACACACATTTGAGAGC 34 433
    666458 2992 3007 21109 21124 CCATTAGAAAAGCAGG 20 434
    666459 3021 3036 21138 21153 TAGGTGCTTGTTGAAT 50 435
    666460 3031 3046 21148 21163 AGGCACTTACTAGGTG 46 436
    666461 3039 3054 21156 21171 GATACAGCAGGCACTT 37 437
    666462 3046 3061 21163 21178 ATGTAGGGATACAGCA 26 438
    666463 3053 3068 21170 21185 CTGTGTAATGTAGGGA 58 439
    666464 3060 3075 21177 21192 GGCTGAACTGTGTAAT 28 440
    666465 3067 3082 21184 21199 TGATAAAGGCTGAACT 59 441
    666466 3074 3089 21191 21206 CTAAGCTTGATAAAGG 46 442
    666467 3085 3100 21202 21217 CTCACTGCTCACTAAG 36 443
    666468 3092 3107 21209 21224 TTCAGTGCTCACTGCT 31 444
    666469 3099 3114 21216 21231 ATAATGTTTCAGTGCT 24 445
    666470 3136 3151 21253 21268 CTGACTTTAATATTAG 44 446
    666471 3178 3193 21295 21310 GTCTTTTCTGTAGTTA 10 447
    666472 3192 3207 21309 21324 GTTCTCTACTGTTTGT 32 448
    666473 3239 3254 21356 21371 GGAGAATTTGGGCTGG 25 449
    666474 3246 3261 21363 21378 TTAGAGAGGAGAATTT 65 450
    666475 3253 3268 21370 21385 GACACTTTTAGAGAGG 13 451
    666476 3260 3275 21377 21392 TCTTGTGGACACTTTT 35 452
    666477 3267 3282 21384 21399 CACCCCTTCTTGTGGA 60 453
    666478 3274 3289 21391 21406 GAATAAACACCCCTTC 56 454
    666479 3288 3303 21405 21420 GAAATGTGTTGGAAGA 32 455
    666480 3335 3350 21452 21467 ACTCCATGAGGTTTTC 27 456
    666481 3337 3352 21454 21469 TGACTCCATGAGGTTT 35 457
    666482 3339 3354 21456 21471 GATGACTCCATGAGGT 33 458
    666483 3341 3356 21458 21473 AAGATGACTCCATGAG 36 459
    666485 3355 3370 21472 21487 ATGAAAGTGTGTGCAA 36 460
    666486 3362 3377 21479 21494 GCACTGCATGAAAGTG 60 461
    666487 3371 3386 21488 21503 CTACAAAGAGCACTGC 47 462
    666488 3378 3393 21495 21510 CTGTTAGCTACAAAGA 44 463
    666489 3385 3400 21502 21517 ATCTTCACTGTTAGCT 26 464
    666490 3392 3407 21509 21524 GAGGTAAATCTTCACT 30 465
    666491 3399 3414 21516 21531 GCAGAACGAGGTAAAT 38 466
    666492 3406 3421 21523 21538 CCTCTGAGCAGAACGA 24 467
    666493 3413 3428 21530 21545 AGCAAGGCCTCTGAGC 45 468
    666494 3420 3435 21537 21552 GCTCCACAGCAAGGCC 42 469
    666495 3427 3442 21544 21559 CAGTGGAGCTCCACAG 59 470
    666496 3432 3447 21549 21564 CATGGCAGTGGAGCTC 13 471
    666497 3434 3449 21551 21566 TACATGGCAGTGGAGC 29 472
    666498 3436 3451 21553 21568 GGTACATGGCAGTGGA 13 473
    666499 3438 3453 21555 21570 TGGGTACATGGCAGTG 26 474
    666500 3440 3455 21557 21572 ACTGGGTACATGGCAG 41 475
    666501 3442 3457 21559 21574 CTACTGGGTACATGGC 16 476
    666502 3448 3463 21565 21580 CAAACCCTACTGGGTA 68 477
    666503 3455 3470 21572 21587 GAAATGTCAAACCCTA 29 478
    666504 3462 3477 21579 21594 GGCTAATGAAATGTCA 36 479
    666505 3469 3484 21586 21601 GTTGCATGGCTAATGA 39 480
    666506 3476 3491 21593 21608 TATCCATGTTGCATGG 39 481
    666507 3491 3506 21608 21623 CTGCTGCCCAATACAT 53 482
    666508 3498 3513 21615 21630 ACACAGTCTGCTGCCC 49 483
    666509 3505 3520 21622 21637 TCACGAAACACAGTCT 32 484
    666510 3512 3527 21629 21644 CTGCAGTTCACGAAAC 62 485
    666511 3519 3534 21636 21651 TACATCACTGCAGTTC 32 486
    666512 3526 3541 21643 21658 AGATGTATACATCACT 24 487
    666513 3548 3563 21665 21680 CCCAAAATACTTTGCA 36 488
    666514 3558 3573 21675 21690 GATAATATACCCCAAA 67 489
    666515 3565 3580 21682 21697 CCCTTAGGATAATATA 51 490
    666516 3572 3587 21689 21704 TTATCTTCCCTTAGGA 72 491
    666517 3599 3614 21716 21731 GTGAAACAGCAGTTCT 38 492
    666518 3606 3621 21723 21738 GGGCCCCGTGAAACAG 67 493
    666519 3613 3628 21730 21745 CAGGTAAGGGCCCCGT 30 494
    666520 3620 3635 21737 21752 AGGGTCACAGGTAAGG 32 495
    666521 3627 3642 21744 21759 AGCAAAGAGGGTCACA 32 496
    666522 3642 3657 21759 21774 GGTTAAATATTCTTCA 52 497
    666523 3661 3676 21778 21793 TCTTTGAAGTGCTGTG 43 498
    666524 3668 3683 21785 21800 GACAGCTTCTTTGAAG 64 499
    666525 3675 3690 21792 21807 CTTCCAAGACAGCTTC 37 500
    666526 3682 3697 21799 21814 AGACAGACTTCCAAGA 64 501
    666527 3689 3704 21806 21821 GCTCCTGAGACAGACT 44 502
    666528 3696 3711 21813 21828 ACAGGGTGCTCCTGAG 77 503
    666529 3710 3725 21827 21842 GGAGAATTAAGAAGAC 68 504
    666530 3721 3736 21838 21853 AGCATCCGCTTGGAGA 63 505
    666531 3728 3743 21845 21860 GAAATGGAGCATCCGC 68 506
    666532 3735 3750 21852 21867 AGCAATTGAAATGGAG 78 507
  • TABLE 9
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence (% UTC) ID NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 20 195
    666533 3742 3757 21859 21874 GTCACAAAGCAATTGA 33 508
    666534 3786 3801 21903 21918 CACTGTTAAAGCAGCA 19 509
    666535 3793 3808 21910 21925 TCAGCTCCACTGTTAA 27 510
    666537 3824 3839 21941 21956 GGCCCCAGCCAAGAAG 92 511
    666538 3831 3846 21948 21963 AGGTAGTGGCCCCAGC 40 512
    666539 3865 3880 21982 21997 GTCAACATACACATAG 42 513
    666540 3886 3901 22003 22018 GATCACTCAGAATTTT 50 514
    666541 3893 3908 22010 22025 TACCCTGGATCACTCA 35 515
    666542 3900 3915 22017 22032 TAGGTCATACCCTGGA 28 516
    666543 3907 3922 22024 22039 CATTCCCTAGGTCATA 46 517
    666544 3915 3930 22032 22047 AGCTAGTTCATTCCCT 52 518
    666545 3922 3937 22039 22054 ATTTCATAGCTAGTTC 56 519
    666546 3929 3944 22046 22061 CCTGAGTATTTCATAG 58 520
    666547 3936 3951 22053 22068 TCCTAACCCTGAGTAT 73 521
    666548 3950 3965 22067 22082 ACAAGTGCTAGGATTC 33 522
    666549 3957 3972 22074 22089 TCCTGAGACAAGTGCT 45 523
    666550 3964 3979 22081 22096 TTCAGAGTCCTGAGAC 54 524
    666551 3968 3983 22085 22100 CCTTTTCAGAGTCCTG 42 525
    666552 3972 3987 22089 22104 CGTTCCTTTTCAGAGT 70 526
    666553 3974 3989 22091 22106 GCCGTTCCTTTTCAGA 38 527
    666554 3976 3991 22093 22108 AAGCCGTTCCTTTTCA 71 528
    666555 3982 3997 22099 22114 ATGAGGAAGCCGTTCC 42 529
    666556 3996 4011 22113 22128 TATCAAGACAAGGAAT 93 530
    666557 4003 4018 22120 22135 TCCACTTTATCAAGAC 35 531
    666559 4017 4032 22134 22149 TCTAGTTTGCCAATTC 38 532
    666560 4024 4039 22141 22156 ACTAAATTCTAGTTTG 100 533
    666561 4035 4050 22152 22167 ACTGAGTACAAACTAA 68 534
    666562 4042 4057 22159 22174 ACTGTCCACTGAGTAC 39 535
    666563 4049 4064 22166 22181 CAACAGCACTGTCCAC 57 536
    666564 4056 4071 22173 22188 AAATCTTCAACAGCAC 55 537
    666565 4063 4078 22180 22195 AGTCCTCAAATCTTCA 46 538
    666566 4071 4086 22188 22203 CTTTAACAAGTCCTCA 48 539
    666567 4078 4093 22195 22210 CAGTGCTCTTTAACAA 63 540
    666568 4085 4100 22202 22217 TATGACCCAGTGCTCT 60 541
    666569 4093 4108 22210 22225 TTTTTCCATATGACCC 25 542
    666570 4107 4122 22224 22239 GGAGACACATACATTT 78 543
    666571 4117 4132 22234 22249 AATGCACCTGGGAGAC 38 544
    666572 4124 4139 22241 22256 ACCAAGAAATGCACCT 43 545
    666573 4134 4149 22251 22266 CAAGACATAAACCAAG 49 546
    666574 4169 4184 22286 22301 CTTGAGGTTTTCCTAA 60 547
    666575 4171 4186 22288 22303 TGCTTGAGGTTTTCCT 20 548
    666576 4177 4192 22294 22309 AATTACTGCTTGAGGT 42 549
    666577 4185 4200 22302 22317 GAGATATTAATTACTG 37 550
    666578 4192 4207 22309 22324 GTTCCAGGAGATATTA 48 551
    666579 4199 4214 22316 22331 CTATAGTGTTCCAGGA 34 552
    666580 4206 4221 22323 22338 TGGTTCTCTATAGTGT 29 553
    666581 4213 4228 22330 22345 GGTCACTTGGTTCTCT 21 554
    666582 4220 4235 22337 22352 ATGAGTCGGTCACTTG 22 555
    666583 4221 4236 22338 22353 AATGAGTCGGTCACTT 54 556
    666584 4223 4238 22340 22355 TAAATGAGTCGGTCAC 24 557
    666585 4225 4240 22342 22357 TGTAAATGAGTCGGTC 31 558
    666586 4227 4242 22344 22359 GTTGTAAATGAGTCGG 13 559
    666587 4229 4244 22346 22361 CAGTTGTAAATGAGTC 11 560
    666588 4231 4246 22348 22363 TTCAGTTGTAAATGAG 44 561
    666589 4237 4252 22354 22369 CTAGGTTTCAGTTGTA 46 562
    666590 4244 4259 22361 22376 GGGCTTCCTAGGTTTC 61 563
    666591 4272 4287 22389 22404 AACTCTCCTGTTTTCG 58 564
    666592 4279 4294 22396 22411 GGCGACTAACTCTCCT 37 565
    666593 4286 4301 22403 22418 TCTGTAGGGCGACTAA 35 566
    666594 4294 4309 22411 22426 CTGGGTTTTCTGTAGG 52 567
    666595 4301 4316 22418 22433 AGTCTAGCTGGGTTTT 37 568
    666596 4308 4323 22425 22440 ACCCAATAGTCTAGCT 75 569
    666598 4322 4337 22439 22454 TCTTTTTAGTTCATAC 74 570
    666599 4330 4345 22447 22462 GCACAGTCTCTTTTTA 64 571
    666600 4337 4352 22454 22469 CACCATGGCACAGTCT 21 572
    666601 4344 4359 22461 22476 TTTTTCTCACCATGGC 26 573
    666602 4365 4380 22482 22497 ATTTCACTGTAGGATT 62 574
    666603 4372 4387 22489 22504 GCTGCTCATTTCACTG 59 575
    666604 4379 4394 22496 22511 TGTAAGGGCTGCTCAT 51 576
    666605 4386 4401 22503 22518 ACAATACTGTAAGGGC 25 577
    666607 4407 4422 22524 22539 ACCTACCTGCCCTTGG 72 578
    666608 4414 4429 22531 22546 CACTAATACCTACCTG 94 579
    666609 4425 4440 22542 22557 GCTTTTTCAAACACTA 32 580
  • TABLE 10
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence (% UTC) ID NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 25 195
    666610 4434 4449 22551 22566 CAAAGACCAGCTTTTT 50 581
    666611 4441 4456 22558 22573 CCTCGCTCAAAGACCA 50 582
    666612 4448 4463 22565 22580 TTTATGCCCTCGCTCA 76 583
    666613 4455 4470 22572 22587 AGCTGTATTTATGCCC 42 584
    666614 4474 4489 22591 22606 TTGTTCCACCCCTGGG 53 585
    666615 4483 4498 22600 22615 CTCCCAGAGTTGTTCC 66 586
    666616 4491 4506 22608 22623 ACCCAAGACTCCCAGA 55 587
    666617 4498 4513 22615 22630 TGCGAGTACCCAAGAC 41 588
    666618 4505 4520 22622 22637 CAAGAGGTGCGAGTAC 78 589
    666619 4520 4535 22637 22652 GAGCATCAACAAAGCC 42 590
    666620 4527 4542 22644 22659 CCTGGCGGAGCATCAA 58 591
    666621 4534 4549 22651 22666 TGGCCTTCCTGGCGGA 91 592
    666622 4541 4556 22658 22673 ACACAAGTGGCCTTCC 69 593
    666623 4575 4590 22692 22707 CTGAATTGTTACTAAA 79 594
    666624 4582 4597 22699 22714 ACTGGATCTGAATTGT 43 595
    666625 4589 4604 22706 22721 AGTTTACACTGGATCT 26 596
    666626 4603 4618 22720 22735 GAGCAATGAACGGAAG 28 597
    666627 4612 4627 22729 22744 GTGACTGGAGAGCAAT 26 598
    666628 4641 4656 22758 22773 AACTTTCACCTGTGGG 50 599
    666629 4669 4684 22786 22801 CCTTAACCAATCCCAA 57 600
    666630 4676 4691 22793 22808 ATAAAGACCTTAACCA 73 601
    666631 4686 4701 22803 22818 CGTAATACAAATAAAG 97 602
    666632 4719 4734 22836 22851 GATGCAGCTGGCCACA 27 603
    666633 4731 4746 22848 22863 ACCATTCAGACAGATG 70 604
    666634 4738 4753 22855 22870 TTCACGCACCATTCAG 84 605
    666635 4745 4760 22862 22877 GAGAGCCTTCACGCAC 77 606
    666636 4752 4767 22869 22884 AAGGTCTGAGAGCCTT 83 607
    666637 4759 4774 22876 22891 GGTGTGTAAGGTCTGA 59 608
    666638 4766 4781 22883 22898 ACAAAATGGTGTGTAA 93 609
    666639 4780 4795 22897 22912 GTAAAACATAACTTAC 92 610
    666640 4807 4822 22924 22939 TCGAGATCAGTCTCAA 18 611
    666641 4814 4829 22931 22946 ACCTGCATCGAGATCA 47 612
    666642 4825 4840 22942 22957 CAAGGAGATCCACCTG 121 613
    666643 4836 4851 22953 22968 TATCAGGATCTCAAGG 94 614
    666644 4843 4858 22960 22975 AACAGGCTATCAGGAT 83 615
    666645 4850 4865 22967 22982 TTCCTGTAACAGGCTA 23 616
    666646 4866 4881 22983 22998 ACTGACCTTTACTTCA 57 617
    666647 4898 4913 23015 23030 CCTCAAAGCTGTGAAA 80 618
    666648 4905 4920 23022 23037 GCATGTTCCTCAAAGC 24 619
    666649 4912 4927 23029 23044 TTCTTATGCATGTTCC 20 620
    666650 4919 4934 23036 23051 GCTACATTTCTTATGC 80 621
    666651 4927 4942 23044 23059 CTACTTCAGCTACATT 53 622
    666652 4934 4949 23051 23066 GTCCCCTCTACTTCAG 59 623
    666653 4949 4964 23066 23081 TGGCCCTTCTCTCACG 89 624
    666654 4956 4971 23073 23088 GCCGGCCTGGCCCTTC 114 625
    666655 4963 4978 23080 23095 TTGGCCTGCCGGCCTG 96 626
    666656 4970 4985 23087 23102 AGGAGGGTTGGCCTGC 96 627
    666657 4977 4992 23094 23109 CCATTGGAGGAGGGTT 68 628
    666658 4982 4997 23099 23114 AATTTCCATTGGAGGA 67 629
    666659 4984 4999 23101 23116 GGAATTTCCATTGGAG 56 630
    666660 4986 5001 23103 23118 CGGGAATTTCCATTGG 50 631
    666661 4988 5003 23105 23120 CACGGGAATTTCCATT 29 632
    666662 4990 5005 23107 23122 AACACGGGAATTTCCA 27 633
    666663 4992 5007 23109 23124 GCAACACGGGAATTTC 26 634
    666664 5005 5020 23122 23137 GTCTCAGTTTGAAGCA 26 635
    666665 5012 5027 23129 23144 CCCATCTGTCTCAGTT 34 636
    666666 5019 5034 23136 23151 GTTAAGTCCCATCTGT 60 637
    666667 5026 5041 23143 23158 ATTGCCTGTTAAGTCC 27 638
    666668 5086 5101 23203 23218 GGCAGTTCTTTCAGCA 63 639
    666669 5093 5108 23210 23225 ACCTGCTGGCAGTTCT 39 640
    666670 5100 5115 23217 23232 GGGTCCTACCTGCTGG 64 641
    666671 5124 5139 23241 23256 CAAGCTTTCATTTGGG 26 642
    666672 5131 5146 23248 23263 GGAAATTCAAGCTTTC 36 643
    666673 5147 5162 23264 23279 ACGCAGAGCCAGTAGG 50 644
    666674 5149 5164 23266 23281 AAACGCAGAGCCAGTA 63 645
    666675 5151 5166 23268 23283 CAAAACGCAGAGCCAG 42 646
    666676 5171 5186 23288 23303 TCCTTTCCTACAGATC 67 647
    666677 5179 5194 23296 23311 GTGAAGCATCCTTTCC 37 648
    666678 5186 5201 23303 23318 TCAGTTTGTGAAGCAT 11 649
    666679 5193 5208 23310 23325 ATCTACCTCAGTTTGT 58 650
    666680 5200 5215 23317 23332 TAGCATTATCTACCTC 34 651
    666681 5207 5222 23324 23339 GACAGCATAGCATTAT 23 652
    666682 5214 5229 23331 23346 TACCAACGACAGCATA 39 653
    666683 5221 5236 23338 23353 TGATGTATACCAACGA 13 654
    666684 5246 5261 23363 23378 GCAGAGCAATTTACAT 34 655
    666685 5253 5268 23370 23385 TTGCTTTGCAGAGCAA 72 656
  • TABLE 11
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence (% UTC) ID NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 15 195
    666688 N/A N/A 18773 18788 CTTAAGCTAAACTCCT 73 657
    666689 N/A N/A 18780 18795 ATGACGACTTAAGCTA 38 658
    666690 N/A N/A 18803 18818 ATATTAGAGACTGTAT 75 659
    666691 N/A N/A 18817 18832 CTCCATCAATCATGAT 67 660
    666692 N/A N/A 18824 18839 GAATGCTCTCCATCAA 55 661
    666693 N/A N/A 18831 18846 GCAAGCTGAATGCTCT 47 662
    666694 N/A N/A 18838 18853 ATCTAAGGCAAGCTGA 63 663
    666695 N/A N/A 18845 18860 TTACAGCATCTAAGGC 79 664
    666696 N/A N/A 18866 18881 AATGTTCAGCTTTTCC 37 665
    666697 N/A N/A 18873 18888 ACGCCTTAATGTTCAG 23 666
    666699 N/A N/A 22817 22832 GACTTCGGGAGATACG 86 667
    666700 N/A N/A 22824 22839 CACAGAGGACTTCGGG 51 668
    666701 N/A N/A 3917 3932 CCCTTCCCGCTCCGAA 84 669
    666702 N/A N/A 4018 4033 AGGCTCGGGCAGAGCC 99 670
    666703 N/A N/A 4254 4269 GAGCACCGCGCCGGAG 93 671
    666704 N/A N/A 4288 4303 ATGTGGAGCTCCTCCT 80 672
    666705 N/A N/A 4546 4561 GCCCCGAATAGGACCC 79 673
    666706 N/A N/A 4593 4608 CCGGGTTCCTCCACCC 91 674
    666707 N/A N/A 4653 4668 CCTGGCGGCCTCCACG 131 675
    666709 N/A N/A 4856 4871 AGGCTCCTACCCGCCT 94 676
    666710 N/A N/A 4965 4980 TGCCGTGTCAGGGTCG 89 677
    666711 N/A N/A 4993 5008 GAGTCTTTGAGGCTGC 66 678
    666712 N/A N/A 5759 5774 ACAGGCGCGGACGCAC 80 679
    666713 N/A N/A 5867 5882 CGAGAAGAGAGGCTGA 93 680
    666714 N/A N/A 6304 6319 GACACATTTTCTGGGT 36 681
    666715 N/A N/A 7071 7086 GATGCTCAGAATGAAG 57 682
    666716 N/A N/A 7190 7205 CTATGCTGAACCCCAC 99 683
    666717 N/A N/A 7197 7212 AATTCTCCTATGCTGA 87 684
    666718 N/A N/A 7380 7395 AGTGATGAGATATTCC 41 685
    666719 N/A N/A 7519 7534 TCCAGATGCAGATTCC 54 686
    666720 N/A N/A 7536 7551 TCACCTGAAGGATTTG 75 687
    666721 N/A N/A 7731 7746 ATGCATAACACGGTGT 55 688
    666722 N/A N/A 7963 7978 ACACAGCCTCGCCCTC 80 689
    666723 N/A N/A 8094 8109 AGCACCGTGTGGAAAG 43 690
    666724 N/A N/A 8126 8141 ACCCTCCCCAACTTAA 90 691
    666725 N/A N/A 8336 8351 CTGGCACCAAAAGTAC 82 692
    666726 N/A N/A 8539 8554 ACTGGCATTGAGACGG 21 693
    8747 8762
    8851 8866
    8903 8918
    9059 9074
    666727 N/A N/A 8540 8555 CACTGGCATTGAGACG 24 694
    8748 8763
    8852 8867
    8904 8919
    9060 9075
    666728 N/A N/A 8541 8556 GCACTGGCATTGAGAC 27 695
    8749 8764
    8853 8868
    8905 8920
    9061 9076
    666729 N/A N/A 8543 8558 AAGCACTGGCATTGAG 58 696
    8751 8766
    8855 8870
    8907 8922
    9063 9078
    666730 N/A N/A 8544 8559 GAAGCACTGGCATTGA 45 697
    8752 8767
    8856 8871
    8908 8923
    9064 9079
    666731 N/A N/A 8545 8560 AGAAGCACTGGCATTG 55 698
    9065 9080
    666732 N/A N/A 8548 8563 ATAAGAAGCACTGGCA 49 699
    8704 8719
    8808 8823
    8964 8979
    9068 9083
    666733 N/A N/A 8549 8564 GATAAGAAGCACTGGC 37 700
    8705 8720
    8809 8824
    8965 8980
    9069 9084
    666734 N/A N/A 8551 8566 GAGATAAGAAGCACTG 56 701
    8707 8722
    8811 8826
    8967 8982
    9071 9086
    666735 N/A N/A 8553 8568 CTGAGATAAGAAGCAC 63 702
    8709 8724
    8813 8828
    8969 8984
    9073 9088
    666737 N/A N/A 8574 8589 GGTAAAGGAGTGCAGG 54 703
    8626 8641
    8678 8693
    8730 8745
    8834 8849
    8886 8901
    8938 8953
    8990 9005
    9042 9057
    666738 N/A N/A 8591 8606 ACTGGCATCGAGACGG 21 704
    8643 8658
    8695 8710
    8799 8814
    8955 8970
    9007 9022
    666739 N/A N/A 8592 8607 CACTGGCATCGAGACG 39 705
    8644 8659
    8696 8711
    8800 8815
    8956 8971
    9008 9023
    666740 N/A N/A 8594 8609 AGCACTGGCATCGAGA 41 706
    8646 8661
    8698 8713
    8802 8817
    8958 8973
    9010 9025
    666741 N/A N/A 8595 8610 AAGCACTGGCATCGAG 73 707
    8647 8662
    8699 8714
    8803 8818
    8959 8974
    9011 9026
    666742 N/A N/A 8597 8612 GGAAGCACTGGCATCG 45 708
    8649 8664
    9013 9028
    666743 N/A N/A 8600 8615 ATAGGAAGCACTGGCA 58 709
    8652 8667
    8756 8771
    8860 8875
    8912 8927
    9016 9031
    666744 N/A N/A 8601 8616 GATAGGAAGCACTGGC 38 710
    8653 8668
    8757 8772
    8861 8876
    8913 8928
    9017 9032
    666745 N/A N/A 8602 8617 AGATAGGAAGCACTGG 54 711
    8654 8669
    8758 8773
    8862 8877
    8914 8929
    9018 9033
    666746 N/A N/A 8603 8618 GAGATAGGAAGCACTG 52 712
    8655 8670
    8759 8774
    8863 8878
    8915 8930
    9019 9034
    666747 N/A N/A 8604 8619 TGAGATAGGAAGCACT 62 713
    8656 8671
    8760 8775
    8864 8879
    8916 8931
    9020 9035
    666748 N/A N/A 8605 8620 CTGAGATAGGAAGCAC 74 714
    8657 8672
    8761 8776
    8865 8880
    8917 8932
    9021 9036
    666749 N/A N/A 9410 9425 GGATGCCACCATCCCA 105 715
    666750 N/A N/A 9490 9505 GGAGTGATCTCTGTGG 32 716
    666751 N/A N/A 9708 9723 GTAGGTAGGCACCTGT 25 717
    666752 N/A N/A 9796 9811 GAGGGAGCTCATTTTG 76 718
    666753 N/A N/A 9960 9975 AAAGGCCAAATTGCAA 48 719
    666754 N/A N/A 9997 10012 CTGCAGCCAAGGATAA 52 720
    666818 N/A N/A 3925 3940 GGCGCGCTCCCTTCCC 90 721
    666819 N/A N/A 4685 4700 CCCTTCCCCGCGACTC 81 722
    666820 N/A N/A 4717 4732 TTGCCTTCGCTCACTC 78 723
    666821 N/A N/A 5757 5772 AGGCGCGGACGCACGG 69 724
    666822 N/A N/A 6997 7012 CTACCTTTTTTGGCTC 83 725
    666823 N/A N/A 7585 7600 TGCCTTGTGACATAAA 55 726
    666824 N/A N/A 8151 8166 ATATTCCAACAGGCGG 47 727
    666825 N/A N/A 8437 8452 TGAACCCTTCATCAGA 52 728
    666826 N/A N/A 9313 9328 AGACCAGGATTCGCCA 67 729
  • TABLE 12
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence (% UTC) ID NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 23 195
    666755 N/A N/A 10003 10018 CACTACCTGCAGCCAA 69 730
    666756 N/A N/A 10020 10035 AGAGTGGTACACCTCT 78 731
    666757 N/A N/A 10256 10271 GTCTCTACCTACTCCA 59 732
    666758 N/A N/A 10308 10323 AACACCTGATCTTGCT 110 733
    666759 N/A N/A 10366 10381 ACCATGTTCCTGAAGA 56 734
    666760 N/A N/A 10660 10675 CTCTTGTGAGGCAAAG 52 735
    666761 N/A N/A 10712 10727 GCGCCCAATCACCTTC 97 736
    666762 N/A N/A 11002 11017 ATCGAATCTGCCCAAA 74 737
    666763 N/A N/A 11010 11025 AAAGTCCCATCGAATC 87 738
    666764 N/A N/A 11024 11039 CAAAGCAAGTGTCTAA 77 739
    666765 N/A N/A 11070 11085 CTCACACACAGGATGT 82 740
    666767 N/A N/A 11344 11359 GAGGAGGAGGACTTAT 49 741
    666768 N/A N/A 11408 11423 TATTACTCTTAGGCAC 56 742
    666769 N/A N/A 11545 11560 GTGCCTTCTTTATAGT 51 743
    666770 N/A N/A 11551 11566 CTAGAGGTGCCTTCTT 74 744
    666771 N/A N/A 11682 11697 TGCCAGAGGGCAAGAT 98 745
    666772 N/A N/A 11975 11990 GCTGTTTATTTCCTAC 34 746
    666773 N/A N/A 11988 12003 CGAGATATAAATAGCT 42 747
    666774 N/A N/A 11990 12005 GCCGAGATATAAATAG 60 748
    666775 N/A N/A 12032 12047 GCAGGTTTCATTTCAT 56 749
    666776 N/A N/A 12034 12049 GGGCAGGTTTCATTTC 68 750
    666777 N/A N/A 12067 12082 AGAGTGGGTGTTGGCC 75 751
    666779 N/A N/A 12274 12289 ATGGAACCCCAAAATC 76 752
    666780 N/A N/A 12292 12307 GCTGCCACTGGTAACT 74 753
    666781 N/A N/A 12374 12389 TCGCCCATGAGTTGAA 61 754
    666782 N/A N/A 12516 12531 AGTTCATGTAAAGTCT 39 755
    666783 N/A N/A 12865 12880 TCGGTCCACATACCTG 61 756
    666784 N/A N/A 13199 13214 CTTGGAGAAGTCCCGT 61 757
    666785 N/A N/A 13330 13345 CCTGTGGTGGAACTCT 73 758
    666786 N/A N/A 14020 14035 AAGAGGCGACTGCTGA 65 759
    666787 N/A N/A 14028 14043 ACTGTTTTAAGAGGCG 30 760
    666788 N/A N/A 14046 14061 ATAGTGCAATGAAATG 64 761
    666789 N/A N/A 14094 14109 GGGAACCTGAAAAGAG 79 762
    666790 N/A N/A 14338 14353 GAGGTTCGCTGAATTG 70 763
    666791 N/A N/A 14687 14702 ATCTGGATGAGCTTAC 62 764
    666792 N/A N/A 14732 14747 AGCTTAGTTATCTGGG 41 765
    666793 N/A N/A 15213 15228 GAACACCATGCCCAAC 93 766
    666794 N/A N/A 15304 15319 GAGCTCTTCCAGATCC 95 767
    666795 N/A N/A 15596 15611 TAGTCGCGCAAGTCTA 108 768
    666796 N/A N/A 15777 15792 ATCCTTAATTATGCAG 61 769
    666797 N/A N/A 15790 15805 GTGTTTGGTGGGAATC 54 770
    666798 N/A N/A 15985 16000 CTAACTTACAGGACTA 69 771
    666799 N/A N/A 16059 16074 TAGTGCTGTGCAGACC 68 772
    666800 N/A N/A 16069 16084 GGGCTGTCCCTAGTGC 109 773
    666801 N/A N/A 16171 16186 AATGTCACGCCCGCAA 81 774
    666802 N/A N/A 16340 16355 GGCCTCCCGCTTGTGG 118 775
    666803 N/A N/A 16383 16398 GAACAGTAACTTGACT 96 776
    666804 N/A N/A 16419 16434 AACTCTGAGTAGACTT 72 777
    666805 N/A N/A 16471 16486 GAGCACCAGCCATCGG 77 778
    666806 N/A N/A 16649 16664 GACCAATTTATGCCAT 62 779
    666807 N/A N/A 16664 16679 CACGCAATGGCAAAAG 81 780
    666808 N/A N/A 16824 16839 TCCTTTGGGTGCTTTC 68 781
    666809 N/A N/A 16888 16903 CTCTTACTCCGCTGAG 105 782
    666810 N/A N/A 16953 16968 ACACACCAGGTTAAAC 88 783
    666811 N/A N/A 17135 17150 AGTGTAACTGAGGACT 107 784
    666812 N/A N/A 17740 17755 TGTTACTTGCCACAGT 61 785
    666813 N/A N/A 17916 17931 ATGCAAGCCCGTTAAT 96 786
    666814 N/A N/A 17966 17981 ATGAGAACTTTGATGT 85 787
    666815 N/A N/A 18136 18151 AAGTCAATCACTGGAG 39 788
    666816 N/A N/A 18196 18211 TTAGCAATTCCTGTTG 80 789
    666817 N/A N/A 18938 18953 GCTAACTGGCCTCAAA 91 790
    666827 N/A N/A 10288 10303 CTTCATTTACTGTTAC 69 791
    666828 N/A N/A 10484 10499 CAACAGAGCTGAGAGT 80 792
    666829 N/A N/A 11844 11859 CTCACGAGCACCTCAG 58 793
    666830 N/A N/A 13244 13259 CTTGTCTCCCCCAGAG 97 794
    666831 N/A N/A 13798 13813 CCACCTCCATTCTAAC 115 795
    666832 N/A N/A 14081 14096 GAGCCGCCACATCAGC 77 796
    666833 N/A N/A 14193 14208 CCACCCTCCGTCTCAC 67 797
    666834 N/A N/A 14242 14257 TATAGCACTCTCCTAT 98 798
    666836 N/A N/A 16203 16218 CAAGACAAATCTTCTG 87 799
    666837 N/A N/A 16641 16656 TATGCCATGGACAAGT 81 800
    666838 N/A N/A 16948 16963 CCAGGTTAAACAGGAA 94 801
    666839 N/A N/A 19232 19247 GACTTAATTCTGGGTT 65 802
    666840 N/A N/A 19412 19427 ACTGAGATATCCTGCA 81 803
  • Example 5: Effect of 3-10-3 cEt Gapmers with Phosphorothioate Internucleoside Linkages on Human IRF4 In Vitro, Single Dose
  • Modified oligonucleotides complementary to a human IRF4 nucleic acid were designed and tested for their effect on IRF4 mRNA in vitro.
  • Cultured SK-MEL-28 cells at a density of 20,000 cells per well were transfected using electroporation with 4,000 nM concentration of modified oligonucleotide or no modified oligonucleotide for untreated controls. After approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by quantitative real-time PCR. Human primer probe set RTS3114 (described hereinabove in Example 1) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN®. Results are presented in the table below as percent control of the amount of IRF4 mRNA, relative to untreated control (UTC) cells.
  • The modified oligonucleotides in Tables 13 through 24 are 3-10-3 cEt gapmers. The gapmers are 16 nucleobases in length, wherein the central gap segment comprises ten 2′-deoxynucleosides and is flanked by wing segments on both the 5′ end and on the 3′ end comprising three cEt nucleosides. The sugar motif for the gapmers is (from 5′ to 3′): kkkddddddddddkkk; wherein represents a 2′-deoxyribose sugar and ‘k’ represents a cEt modified sugar. Each internucleoside linkage is a phosphorothioate internucleoside linkage and each cytosine residue is a 5-methylcytosine. “Start Site” indicates the 5′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence. “Stop Site” indicates the 3′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Each modified oligonucleotide listed in Tables 13 through 24 below is complementary to human IRF4 nucleic acid sequences SEQ ID NO: 1 or SEQ ID NO: 2, as indicated. ‘N/A’ indicates that the modified oligonucleotide is not complementary to that particular nucleic acid sequence with 100% complementarity. As shown below, modified oligonucleotides complementary to human IRF4 reduced the amount of human IRF4 mRNA.
  • TABLE 13
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence (% UTC) ID NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 24 195
    881075 2 17 3741 3756 AACTGAGAGTGCGAGG 99 804
    881099 342 357 6821 6836 AAACAGTGCCCAAGCC 75 805
    881122 624 639 9114 9129 CATCATGTAGTTGTGA 59 806
    881169 1192 1207 13745 13760 TGTCAAAGAGCTTGCA 89 807
    881193 1416 1431 19533 19548 GCTGATGTGTTCTGGT 21 808
    881217 1740 1755 19857 19872 CAGTAAGAGGGCAGTC 50 809
    881241 1927 1942 20044 20059 CATCACTTGGTCAATT 71 810
    881265 2042 2057 20159 20174 CCTACAAGCAGTCATC 46 811
    881289 2194 2209 20311 20326 CTACAGGCACGGCTTC 48 812
    881313 2385 2400 20502 20517 TACTAGATTGTAGGAC 73 813
    881337 2512 2527 20629 20644 CAACAGTTCAAGTATT 65 814
    881361 2665 2680 20782 20797 TTCCAGTGGTGGGTCC 71 815
    881385 2826 2841 20943 20958 CAAGTGGAGGTCTTTG 33 816
    881409 2911 2926 21028 21043 ATGAGAAACGGCCTGG 36 817
    881433 3047 3062 21164 21179 AATGTAGGGATACAGC 38 818
    881457 3273 3288 21390 21405 AATAAACACCCCTTCT 79 819
    881481 3419 3434 21536 21551 CTCCACAGCAAGGCCT 49 820
    881505 3507 3522 21624 21639 GTTCACGAAACACAGT 37 821
    881528 3625 3640 21742 21757 CAAAGAGGGTCACAGG 37 822
    881552 3903 3918 22020 22035 CCCTAGGTCATACCCT 43 823
    881576 4052 4067 22169 22184 CTTCAACAGCACTGTC 44 824
    881595 4285 4300 22402 22417 CTGTAGGGCGACTAAC 51 825
    881619 4412 4427 22529 22544 CTAATACCTACCTGCC 53 826
    881643 4545 4560 22662 22677 GCACACACAAGTGGCC 36 827
    881667 4602 4617 22719 22734 AGCAATGAACGGAAGT 20 828
    881691 4839 4854 22956 22971 GGCTATCAGGATCTCA 55 829
    881715 5030 5045 23147 23162 CCCCATTGCCTGTTAA 80 830
    881739 5206 5221 23323 23338 ACAGCATAGCATTATC 36 831
    881763 N/A N/A 18778 18793 GACGACTTAAGCTAAA 38 832
    881787 N/A N/A 18847 18862 ATTTACAGCATCTAAG 53 833
    881809 N/A N/A 4075 4090 GCTCATCCCGTCCAGC 85 834
    881832 N/A N/A 4402 4417 GGAGAGCGGAGGCGGG 79 835
    881855 N/A N/A 4644 4659 CTCCACGCGCGGAGGA 101 836
    881879 N/A N/A 5038 5053 GGGCACCCCGCCCCGA 99 837
    881903 N/A N/A 5660 5675 GCACGGACGAACGCGC 77 838
    881925 N/A N/A 5777 5792 ACGAAAACAGCCGCCG 86 839
    881947 N/A N/A 6136 6151 GAGCAAATTGAGACCA 45 840
    881971 N/A N/A 6415 6430 GCGCATAGGTCCTTCA 37 841
    881993 N/A N/A 7155 7170 CCACATAACTCAGGCA 30 842
    882017 N/A N/A 7376 7391 ATGAGATATTCCTCTC 68 843
    882041 N/A N/A 7696 7711 CAGCAACTCCCTTGGG 77 844
    882065 N/A N/A 8145 8160 CAACAGGCGGACACGC 58 845
    882088 N/A N/A 8385 8400 ATGGAGATACTTGTAC 38 846
    882112 N/A N/A 8554 8569 GCTGAGATAAGAAGCA 68 847
    8710 8725
    8814 8829
    8970 8985
    9074 9089
    882135 N/A N/A 9362 9377 GCACACGCAGCCTCTA 95 848
    882158 N/A N/A 9606 9621 CCACTATTCGAGAGAA 43 849
    882182 N/A N/A 9981 9996 CCTGAACATGACTGGG 62 850
    882205 N/A N/A 10162 10177 GAATTTCAGGAGCTAG 39 851
    882229 N/A N/A 10314 10329 GCACAGAACACCTGAT 44 852
    882253 N/A N/A 10616 10631 AGCTGATGGAGAAACG 90 853
    882277 N/A N/A 11088 11103 CTAAATCACCCTGGTC 53 854
    882301 N/A N/A 11366 11381 GAACTAATGTCCCCAG 39 855
    882325 N/A N/A 11666 11681 GAGAATTCCAAACCTT 24 856
    882349 N/A N/A 11940 11955 GTCTTAGGTGTTCAAG 44 857
    882373 N/A N/A 12157 12172 CAGCAGGTTTTGAGAC 80 858
    882397 N/A N/A 12512 12527 CATGTAAAGTCTGCTG 42 859
    882420 N/A N/A 12893 12908 ATATAACGGTGTTTCA 42 860
    882443 N/A N/A 13175 13190 ACCCATTTAATCTGTC 43 861
    882465 N/A N/A 13791 13806 CATTCTAACAGATAAC 102 862
    882487 N/A N/A 14150 14165 ACACACCTGACAACCA 64 863
    882510 N/A N/A 14374 14389 GCATGACAGGGCGAGG 57 864
    882533 N/A N/A 14708 14723 TGCTTTGGGCACCAAA 48 865
    882557 N/A N/A 15460 15475 GCCCAGCAAGAGGCAC 93 866
    882580 N/A N/A 15804 15819 TAGATAACATGAGAGT 50 867
    882603 N/A N/A 15925 15940 CAAATGACTTAGTCAG 45 868
    882627 N/A N/A 16168 16183 GTCACGCCCGCAAAAG 61 869
    882650 N/A N/A 16388 16403 GGATGGAACAGTAACT 48 870
    882674 N/A N/A 16667 16682 AGTCACGCAATGGCAA 50 871
    882698 N/A N/A 16900 16915 GAGGAATGAGCACTCT 74 872
    882722 N/A N/A 17238 17253 GGTTACGCTTATTTTT 36 873
    882746 N/A N/A 17493 17508 GCTAGATAGCATTCTT 44 874
    882770 N/A N/A 17733 17748 TGCCACAGTTGAACCC 50 875
    882794 N/A N/A 17987 18002 TAGCATCAGAGCTAGA 51 876
    882817 N/A N/A 18582 18597 CTGGATTGATGTGATA 57 877
    882841 N/A N/A 18961 18976 ACTACTATTGTGGAAA 82 878
    882864 N/A N/A 19234 19249 GTGACTTAATTCTGGG 49 879
  • TABLE 14
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2  SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence (% UTC) ID NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 14 195
    881076 6 21 3745 3760 GTGAAACTGAGAGTGC 120 880
    881100 343 358 6822 6837 TAAACAGTGCCCAAGC 59 881
    881123 682 697 9172 9187 GGATTTCCGGGTGTGG 39 882
    881170 1206 1221 13759 13774 CAAGAACTGCTGTGTG 105 883
    881194 1432 1447 19549 19564 GGTAATCTTCTGGATT 70 884
    881218 1741 1756 19858 19873 ACAGTAAGAGGGCAGT 16 885
    881242 1930 1945 20047 20062 ACACATCACTTGGTCA 22 886
    881266 2043 2058 20160 20175 ACCTACAAGCAGTCAT 54 887
    881290 2195 2210 20312 20327 GCTACAGGCACGGCTT 16 888
    881314 2387 2402 20504 20519 ATTACTAGATTGTAGG 50 889
    881338 2515 2530 20632 20647 GGGCAACAGTTCAAGT 64 890
    881362 2686 2701 20803 20818 CCGTAGTCAGCTCCAT 27 891
    881386 2828 2843 20945 20960 AGCAAGTGGAGGTCTT 37 892
    881410 2912 2927 21029 21044 TATGAGAAACGGCCTG 55 893
    881434 3048 3063 21165 21180 TAATGTAGGGATACAG 22 894
    881458 3275 3290 21392 21407 AGAATAAACACCCCTT 26 895
    881482 3429 3444 21546 21561 GGCAGTGGAGCTCCAC 27 896
    881506 3510 3525 21627 21642 GCAGTTCACGAAACAC 20 897
    881529 3628 3643 21745 21760 CAGCAAAGAGGGTCAC 39 898
    881553 3904 3919 22021 22036 TCCCTAGGTCATACCC 42 899
    881577 4058 4073 22175 22190 TCAAATCTTCAACAGC 24 900
    881596 4300 4315 22417 22432 GTCTAGCTGGGTTTTC 37 901
    881620 4413 4428 22530 22545 ACTAATACCTACCTGC 52 902
    881644 4547 4562 22664 22679 ACGCACACACAAGTGG 41 903
    881668 4608 4623 22725 22740 CTGGAGAGCAATGAAC 33 904
    881692 4844 4859 22961 22976 TAACAGGCTATCAGGA 74 905
    881716 5040 5055 23157 23172 GGGAAGTGGACCCCAT 91 906
    881740 5208 5223 23325 23340 CGACAGCATAGCATTA 25 907
    881764 N/A N/A 18782 18797 ATATGACGACTTAAGC 62 908
    881788 N/A N/A 18849 18864 GAATTTACAGCATCTA 24 909
    881810 N/A N/A 4084 4099 GTCCGGTTAGCTCATC 55 910
    881833 N/A N/A 4403 4418 GGGAGAGCGGAGGCGG 78 911
    881856 N/A N/A 4703 4718 TCCCAACCCGCTTCTC 86 912
    881880 N/A N/A 5056 5071 CACGAGGCACCGCACT 113 913
    881904 N/A N/A 5664 5679 GAACGCACGGACGAAC 82 914
    881926 N/A N/A 5778 5793 GACGAAAACAGCCGCC 38 915
    881948 N/A N/A 6141 6156 TCTGAGAGCAAATTGA 71 916
    881994 N/A N/A 7157 7172 ACCCACATAACTCAGG 69 917
    882018 N/A N/A 7384 7399 GCATAGTGATGAGATA 41 918
    882042 N/A N/A 7717 7732 GTTGACAAATAAGGTA 40 919
    882066 N/A N/A 8146 8161 CCAACAGGCGGACACG 17 920
    882089 N/A N/A 8391 8406 AGGACAATGGAGATAC 28 921
    882113 N/A N/A 8566 8581 AGTGCAGGAGAGGCTG 64 922
    8618 8633
    8670 8685
    8722 8737
    8774 8789
    8826 8841
    8878 8893
    8930 8945
    8982 8997
    9034 9049
    9086 9101
    882136 N/A N/A 9386 9401 AGAAAACCCCCCTCTC 77 923
    882159 N/A N/A 9608 9623 CACCACTATTCGAGAG 52 924
    882183 N/A N/A 9986 10001 GATAACCTGAACATGA 83 925
    882206 N/A N/A 10172 10187 ACGCAAGTCTGAATTT 35 926
    882230 N/A N/A 10352 10367 GACAATGTTGTATGAA 28 927
    882254 N/A N/A 10634 10649 GACCAACTGGAAAACC 44 928
    882278 N/A N/A 11089 11104 CCTAAATCACCCTGGT 73 929
    882302 N/A N/A 11368 11383 CAGAACTAATGTCCCC 31 930
    882326 N/A N/A 11669 11684 GATGAGAATTCCAAAC 16 931
    882350 N/A N/A 11950 11965 ACCCACACAAGTCTTA 104 932
    882374 N/A N/A 12161 12176 TCAACAGCAGGTTTTG 59 933
    882398 N/A N/A 12515 12530 GTTCATGTAAAGTCTG 14 934
    882421 N/A N/A 12896 12911 AAAATATAACGGTGTT 69 935
    882444 N/A N/A 13196 13211 GGAGAAGTCCCGTGGA 41 936
    882466 N/A N/A 13881 13896 CGCCGAAGTCAACAGG 56 937
    882488 N/A N/A 14160 14175 CATGAGGGTGACACAC 53 938
    882511 N/A N/A 14376 14391 CAGCATGACAGGGCGA 44 939
    882534 N/A N/A 14716 14731 GACATATTTGCTTTGG 42 940
    882558 N/A N/A 15497 15512 AGCTTAGTCACCACGG 33 941
    882581 N/A N/A 15805 15820 CTAGATAACATGAGAG 47 942
    882604 N/A N/A 15926 15941 CCAAATGACTTAGTCA 49 943
    882628 N/A N/A 16177 16192 CAATAAAATGTCACGC 53 944
    882651 N/A N/A 16390 16405 AGGGATGGAACAGTAA 53 945
    882675 N/A N/A 16691 16706 CGGGAGATAAAGAACA 69 946
    882699 N/A N/A 16905 16920 TGCAAGAGGAATGAGC 16 947
    882723 N/A N/A 17239 17254 GGGTTACGCTTATTTT 35 948
    882747 N/A N/A 17508 17523 AATGAAGATCCACTAG 39 949
    882771 N/A N/A 17746 17761 TTTTAGTGTTACTTGC 68 950
    882795 N/A N/A 17990 18005 AAATAGCATCAGAGCT 87 951
    882818 N/A N/A 18584 18599 AACTGGATTGATGTGA 23 952
    882842 N/A N/A 18964 18979 AAAACTACTATTGTGG 86 953
    882865 N/A N/A 19240 19255 GCCAAAGTGACTTAAT 30 954
    882898 N/A N/A 6422 6437 AAGAATGGCGCATAGG 19 955
  • TABLE 15
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence (% UTC) ID NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 45 195
    881077 7 22 3746 3761 GGTGAAACTGAGAGTG 92 956
    881101 344 359 6823 6838 TTAAACAGTGCCCAAG 79 957
    881124 689 704 9179 9194 TGGTACGGGATTTCCG 63 958
    881171 1207 1222 13760 13775 ACAAGAACTGCTGTGT 93 959
    881195 1433 1448 19550 19565 TGGTAATCTTCTGGAT 76 960
    881219 1744 1759 19861 19876 AAAACAGTAAGAGGGC 61 961
    881243 1934 1949 20051 20066 GTAAACACATCACTTG 49 962
    881267 2044 2059 20161 20176 TACCTACAAGCAGTCA 44 963
    881291 2196 2211 20313 20328 GGCTACAGGCACGGCT 58 964
    881315 2388 2403 20505 20520 CATTACTAGATTGTAG 91 965
    881339 2520 2535 20637 20652 CAGAAGGGCAACAGTT 62 966
    881363 2701 2716 20818 20833 ACTGAGTGTGCAGTTC 64 967
    881387 2829 2844 20946 20961 AAGCAAGTGGAGGTCT 49 968
    881411 2913 2928 21030 21045 GTATGAGAAACGGCCT 41 969
    881435 3049 3064 21166 21181 GTAATGTAGGGATACA 52 970
    881459 3277 3292 21394 21409 GAAGAATAAACACCCC 48 971
    881483 3430 3445 21547 21562 TGGCAGTGGAGCTCCA 54 972
    881507 3517 3532 21634 21649 CATCACTGCAGTTCAC 53 973
    881530 3631 3646 21748 21763 CTTCAGCAAAGAGGGT 41 974
    881554 3918 3933 22035 22050 CATAGCTAGTTCATTC 65 975
    881578 4089 4104 22206 22221 TCCATATGACCCAGTG 34 976
    881597 4305 4320 22422 22437 CAATAGTCTAGCTGGG 37 977
    881621 4418 4433 22535 22550 CAAACACTAATACCTA 69 978
    881645 4556 4571 22673 22688 GTAACTGACACGCACA 49 979
    881669 4618 4633 22735 22750 GGGCATGTGACTGGAG 50 980
    881693 4845 4860 22962 22977 GTAACAGGCTATCAGG 55 981
    881717 5152 5167 23269 23284 GCAAAACGCAGAGCCA 43 982
    881741 5209 5224 23326 23341 ACGACAGCATAGCATT 33 983
    881765 N/A N/A 18783 18798 TATATGACGACTTAAG 70 984
    881789 N/A N/A 18853 18868 TCCTGAATTTACAGCA 52 985
    881834 N/A N/A 4404 4419 CGGGAGAGCGGAGGCG 100 986
    881857 N/A N/A 4740 4755 CCGCACTCACTCGCAG 92 987
    881881 N/A N/A 5057 5072 CCACGAGGCACCGCAC 119 988
    881905 N/A N/A 5668 5683 ACGAGAACGCACGGAC 60 989
    881927 N/A N/A 5779 5794 AGACGAAAACAGCCGC 75 990
    881949 N/A N/A 6209 6224 ACTAAGGACAGCTGTG 85 991
    881972 N/A N/A 6424 6439 GAAAGAATGGCGCATA 51 992
    881995 N/A N/A 7168 7183 TTCAACTTGTGACCCA 51 993
    882019 N/A N/A 7385 7400 TGCATAGTGATGAGAT 63 994
    882043 N/A N/A 7726 7741 TAACACGGTGTTGACA 65 995
    882067 N/A N/A 8147 8162 TCCAACAGGCGGACAC 71 996
    882090 N/A N/A 8399 8414 GATCATAAAGGACAAT 70 997
    882114 N/A N/A 8570 8585 AAGGAGTGCAGGAGAG 87 998
    8622 8637
    8674 8689
    8726 8741
    8778 8793
    8830 8845
    8882 8897
    8934 8949
    8986 9001
    9038 9053
    9090 9105
    882137 N/A N/A 9387 9402 GAGAAAACCCCCCTCT 83 999
    882160 N/A N/A 9611 9626 ACACACCACTATTCGA 65 1000
    882184 N/A N/A 9990 10005 CAAGGATAACCTGAAC 74 1001
    882207 N/A N/A 10179 10194 GCAGTAAACGCAAGTC 46 1002
    882231 N/A N/A 10357 10372 CTGAAGACAATGTTGT 45 1003
    882255 N/A N/A 10672 10687 TAGCAGGGCACGCTCT 69 1004
    882279 N/A N/A 11090 11105 TCCTAAATCACCCTGG 79 1005
    882303 N/A N/A 11370 11385 ACCAGAACTAATGTCC 68 1006
    882327 N/A N/A 11674 11689 GGCAAGATGAGAATTC 75 1007
    882351 N/A N/A 11987 12002 GAGATATAAATAGCTG 49 1008
    882375 N/A N/A 12175 12190 AACTATCTTATTCCTC 70 1009
    882422 N/A N/A 12897 12912 AAAAATATAACGGTGT 76 1010
    882445 N/A N/A 13203 13218 AACACTTGGAGAAGTC 57 1011
    882467 N/A N/A 13904 13919 AGTCAAGCCCCAAGCC 87 1012
    882489 N/A N/A 14161 14176 GCATGAGGGTGACACA 58 1013
    882512 N/A N/A 14432 14447 TCCCACGCGGGAGGCT 99 1014
    882535 N/A N/A 14717 14732 GGACATATTTGCTTTG 68 1015
    882559 N/A N/A 15501 15516 TTCCAGCTTAGTCACC 63 1016
    882582 N/A N/A 15806 15821 CCTAGATAACATGAGA 74 1017
    882605 N/A N/A 15927 15942 CCCAAATGACTTAGTC 68 1018
    882629 N/A N/A 16178 16193 ACAATAAAATGTCACG 71 1019
    882652 N/A N/A 16394 16409 CTCCAGGGATGGAACA 81 1020
    882676 N/A N/A 16705 16720 GACCACAGTGAAGTCG 86 1021
    882700 N/A N/A 16926 16941 GCTTACTGTGATTCTG 66 1022
    882724 N/A N/A 17241 17256 AAGGGTTACGCTTATT 48 1023
    882748 N/A N/A 17545 17560 ATGGATAGTTTCTCAT 75 1024
    882772 N/A N/A 17760 17775 TCCTAACCCTACCCTT 70 1025
    882796 N/A N/A 17991 18006 GAAATAGCATCAGAGC 55 1026
    882819 N/A N/A 18601 18616 ATCCATGTCAACTTTA 41 1027
    882843 N/A N/A 18965 18980 CAAAACTACTATTGTG 77 1028
    882866 N/A N/A 19241 19256 AGCCAAAGTGACTTAA 42 1029
    882892 N/A N/A 4089 4104 CGACAGTCCGGTTAGC 89 1030
    882904 N/A N/A 12597 12612 TTCCACACTGGATATG 59 1031
  • TABLE 16
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence (% UTC) ID NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 39 195
    881078 14 29 3753 3768 ATCGAGCGGTGAAACT 71 1032
    881102 357 372 6836 6851 TCGGAACTTTCCTTTA 67 1033
    881125 692 707 9182 9197 CATTGGTACGGGATTT 84 1034
    881172 1208 1223 13761 13776 GACAAGAACTGCTGTG 85 1035
    881196 1444 1459 19561 19576 GGATAGATCTGTGGTA 51 1036
    881220 1745 1760 19862 19877 CAAAACAGTAAGAGGG 69 1037
    881244 1950 1965 20067 20082 GCGCATTTCAGTAAAT 67 1038
    881268 2046 2061 20163 20178 CATACCTACAAGCAGT 57 1039
    881292 2199 2214 20316 20331 CAAGGCTACAGGCACG 49 1040
    881316 2389 2404 20506 20521 ACATTACTAGATTGTA 59 1041
    881340 2525 2540 20642 20657 TTGGACAGAAGGGCAA 71 1042
    881364 2710 2725 20827 20842 AAACAGCCCACTGAGT 89 1043
    881388 2830 2845 20947 20962 TAAGCAAGTGGAGGTC 53 1044
    881412 2914 2929 21031 21046 AGTATGAGAAACGGCC 38 1045
    881436 3050 3065 21167 21182 TGTAATGTAGGGATAC 47 1046
    881460 3343 3358 21460 21475 GCAAGATGACTCCATG 37 1047
    881484 3431 3446 21548 21563 ATGGCAGTGGAGCTCC 44 1048
    881508 3520 3535 21637 21652 ATACATCACTGCAGTT 64 1049
    881531 3643 3658 21760 21775 GGGTTAAATATTCTTC 48 1050
    881555 3919 3934 22036 22051 TCATAGCTAGTTCATT 48 1051
    881579 4125 4140 22242 22257 AACCAAGAAATGCACC 67 1052
    881598 4306 4321 22423 22438 CCAATAGTCTAGCTGG 81 1053
    881622 4419 4434 22536 22551 TCAAACACTAATACCT 75 1054
    881646 4557 4572 22674 22689 AGTAACTGACACGCAC 49 1055
    881670 4667 4682 22784 22799 TTAACCAATCCCAACA 70 1056
    881694 4846 4861 22963 22978 TGTAACAGGCTATCAG 69 1057
    881718 5153 5168 23270 23285 AGCAAAACGCAGAGCC 39 1058
    881742 5210 5225 23327 23342 AACGACAGCATAGCAT 26 1059
    881766 N/A N/A 18784 18799 ATATATGACGACTTAA 94 1060
    881790 N/A N/A 18871 18886 GCCTTAATGTTCAGCT 51 1061
    881811 N/A N/A 4126 4141 GCCTTGGACGGCCCCG 77 1062
    881835 N/A N/A 4416 4431 CCGGAGCAGGCCCGGG 113 1063
    881858 N/A N/A 4806 4821 CCGACACGCGCCGCTC 70 1064
    881882 N/A N/A 5059 5074 AGCCACGAGGCACCGC 88 1065
    881906 N/A N/A 5672 5687 GGAAACGAGAACGCAC 70 1066
    881928 N/A N/A 5783 5798 TGAGAGACGAAAACAG 109 1067
    881950 N/A N/A 6216 6231 GCCTAGGACTAAGGAC 67 1068
    881973 N/A N/A 6426 6441 AAGAAAGAATGGCGCA 37 1069
    881996 N/A N/A 7187 7202 TGCTGAACCCCACAGG 67 1070
    882020 N/A N/A 7386 7401 ATGCATAGTGATGAGA 55 1071
    882044 N/A N/A 7728 7743 CATAACACGGTGTTGA 64 1072
    882068 N/A N/A 8148 8163 TTCCAACAGGCGGACA 57 1073
    882091 N/A N/A 8406 8421 CATGGAGGATCATAAA 78 1074
    882115 N/A N/A 8598 8613 AGGAAGCACTGGCATC 43 1075
    8650 8665
    9014 9029
    882138 N/A N/A 9424 9439 TAAACTTGGCTGTGGG 73 1076
    882161 N/A N/A 9632 9647 TTCCAACAATAGCAAC 54 1077
    882208 N/A N/A 10181 10196 GAGCAGTAAACGCAAG 46 1078
    882232 N/A N/A 10367 10382 AACCATGTTCCTGAAG 59 1079
    882256 N/A N/A 10674 10689 ACTAGCAGGGCACGCT 62 1080
    882280 N/A N/A 11101 11116 TCTAATGGTGCTCCTA 49 1081
    882304 N/A N/A 11378 11393 GATGAGGGACCAGAAC 80 1082
    882328 N/A N/A 11675 11690 GGGCAAGATGAGAATT 100 1083
    882352 N/A N/A 11989 12004 CCGAGATATAAATAGC 39 1084
    882376 N/A N/A 12206 12221 TATCATGCATACCAAA 42 1085
    882399 N/A N/A 12654 12669 TGGTAGAATGTGATAT 57 1086
    882423 N/A N/A 12900 12915 GCAAAAAATATAACGG 53 1087
    882446 N/A N/A 13275 13290 CGTCAAGGAGGCCTGG 57 1088
    882468 N/A N/A 13913 13928 CTCTACTGGAGTCAAG 75 1089
    882490 N/A N/A 14162 14177 TGCATGAGGGTGACAC 55 1090
    882513 N/A N/A 14458 14473 GGCGAGTGGCGGGTAG 92 1091
    882536 N/A N/A 14736 14751 CTGAAGCTTAGTTATC 62 1092
    882560 N/A N/A 15515 15530 ACTCAATGTGCACCTT 71 1093
    882583 N/A N/A 15807 15822 CCCTAGATAACATGAG 83 1094
    882606 N/A N/A 15982 15997 ACTTACAGGACTATTT 84 1095
    882630 N/A N/A 16200 16215 GACAAATCTTCTGCCT 74 1096
    882653 N/A N/A 16422 16437 TGTAACTCTGAGTAGA 57 1097
    882677 N/A N/A 16708 16723 GTAGACCACAGTGAAG 71 1098
    882701 N/A N/A 16934 16949 AAGCAAGAGCTTACTG 86 1099
    882725 N/A N/A 17246 17261 AGTTTAAGGGTTACGC 37 1100
    882749 N/A N/A 17546 17561 AATGGATAGTTTCTCA 37 1101
    882773 N/A N/A 17771 17786 TCTAACCCTAATCCTA 95 1102
    882797 N/A N/A 18030 18045 GTTCAAGATTAAACCA 29 1103
    882820 N/A N/A 18605 18620 TTGCATCCATGTCAAC 53 1104
    882844 N/A N/A 19017 19032 GTATAGTTCTCAACCA 53 1105
    882867 N/A N/A 19266 19281 TCCATAGATCAACATG 55 1106
    882903 N/A N/A 9991 10006 CCAAGGATAACCTGAA 56 1107
  • TABLE 17
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence (% UTC) ID NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 37 195
    881079 15 30 3754 3769 GATCGAGCGGTGAAAC 77 1108
    881103 412 427 6891 6906 AAGCGCACCGCAGGCG 96 1109
    881126 694 709 9184 9199 GACATTGGTACGGGAT 64 1110
    881173 1209 1224 13762 13777 TGACAAGAACTGCTGT 82 1111
    881197 1446 1461 19563 19578 GCGGATAGATCTGTGG 45 1112
    881221 1777 1792 19894 19909 CGCTGAACTGAAATCT 63 1113
    881245 1955 1970 20072 20087 AAAGAGCGCATTTCAG 94 1114
    881269 2047 2062 20164 20179 ACATACCTACAAGCAG 55 1115
    881293 2202 2217 20319 20334 CCCCAAGGCTACAGGC 75 1116
    881317 2391 2406 20508 20523 AGACATTACTAGATTG 34 1117
    881341 2530 2545 20647 20662 AGTACTTGGACAGAAG 57 1118
    881365 2740 2755 20857 20872 GAGGAAGCATAGAACA 82 1119
    881389 2832 2847 20949 20964 CTTAAGCAAGTGGAGG 30 1120
    881413 2915 2930 21032 21047 TAGTATGAGAAACGGC 22 1121
    881437 3051 3066 21168 21183 GTGTAATGTAGGGATA 36 1122
    881461 3344 3359 21461 21476 TGCAAGATGACTCCAT 43 1123
    881485 3433 3448 21550 21565 ACATGGCAGTGGAGCT 36 1124
    881509 3522 3537 21639 21654 GTATACATCACTGCAG 56 1125
    881532 3660 3675 21777 21792 CTTTGAAGTGCTGTGT 84 1126
    881556 3920 3935 22037 22052 TTCATAGCTAGTTCAT 56 1127
    881580 4168 4183 22285 22300 TTGAGGTTTTCCTAAA 71 1128
    881599 4307 4322 22424 22439 CCCAATAGTCTAGCTG 44 1129
    881623 4430 4445 22547 22562 GACCAGCTTTTTCAAA 62 1130
    881647 4558 4573 22675 22690 AAGTAACTGACACGCA 77 1131
    881671 4670 4685 22787 22802 ACCTTAACCAATCCCA 29 1132
    881695 4847 4862 22964 22979 CTGTAACAGGCTATCA 56 1133
    881719 5154 5169 23271 23286 CAGCAAAACGCAGAGC 46 1134
    881743 5212 5227 23329 23344 CCAACGACAGCATAGC 24 1135
    881767 N/A N/A 18785 18800 TATATATGACGACTTA 80 1136
    881791 N/A N/A 18872 18887 CGCCTTAATGTTCAGC 34 1137
    881812 N/A N/A 4152 4167 AGGCAGTTGTGCCGTC 162 1138
    881836 N/A N/A 4423 4438 CCGGACCCCGGAGCAG 124 1139
    881859 N/A N/A 4807 4822 CCCGACACGCGCCGCT 88 1140
    881883 N/A N/A 5062 5077 TTCAGCCACGAGGCAC 95 1141
    881907 N/A N/A 5674 5689 GTGGAAACGAGAACGC 97 1142
    881929 N/A N/A 5794 5809 CAGAGACGCGGTGAGA 161 1143
    881951 N/A N/A 6217 6232 TGCCTAGGACTAAGGA 74 1144
    881974 N/A N/A 6479 6494 GCTAAACCCAAAATAC 96 1145
    881997 N/A N/A 7192 7207 TCCTATGCTGAACCCC 64 1146
    882021 N/A N/A 7390 7405 TACCATGCATAGTGAT 56 1147
    882045 N/A N/A 7730 7745 TGCATAACACGGTGTT 62 1148
    882069 N/A N/A 8153 8168 GCATATTCCAACAGGC 34 1149
    882092 N/A N/A 8409 8424 ACTCATGGAGGATCAT 81 1150
    882116 N/A N/A 8599 8614 TAGGAAGCACTGGCAT 72 1151
    8651 8666
    8755 8770
    8859 8874
    8911 8926
    9015 9030
    882139 N/A N/A 9425 9440 GTAAACTTGGCTGTGG 82 1152
    882162 N/A N/A 9669 9684 TGGTATTTTTCCGTTC 31 1153
    882185 N/A N/A 9992 10007 GCCAAGGATAACCTGA 31 1154
    882209 N/A N/A 10186 10201 AGCCAGAGCAGTAAAC 85 1155
    882233 N/A N/A 10371 10386 ACTGAACCATGTTCCT 49 1156
    882257 N/A N/A 10676 10691 CAACTAGCAGGGCACG 62 1157
    882281 N/A N/A 11102 11117 TTCTAATGGTGCTCCT 93 1158
    882305 N/A N/A 11396 11411 GCACATCAATGTTTTA 33 1159
    882329 N/A N/A 11687 11702 AAAGATGCCAGAGGGC 77 1160
    882353 N/A N/A 11991 12006 TGCCGAGATATAAATA 77 1161
    882377 N/A N/A 12207 12222 GTATCATGCATACCAA 35 1162
    882400 N/A N/A 12675 12690 GCCTTAATGGTGATTT 74 1163
    882447 N/A N/A 13289 13304 ACAAAAGGTTCCCGCG 97 1164
    882469 N/A N/A 13921 13936 CAGAAGATCTCTACTG 88 1165
    882491 N/A N/A 14163 14178 CTGCATGAGGGTGACA 81 1166
    882514 N/A N/A 14477 14492 GAAGAGTTGGCGGTGG 85 1167
    882537 N/A N/A 14737 14752 CCTGAAGCTTAGTTAT 65 1168
    882561 N/A N/A 15531 15546 ACGCAGTGCACCTGTG 107 1169
    882584 N/A N/A 15813 15828 CTCCAACCCTAGATAA 98 1170
    882607 N/A N/A 15983 15998 AACTTACAGGACTATT 87 1171
    882631 N/A N/A 16201 16216 AGACAAATCTTCTGCC 104 1172
    882654 N/A N/A 16430 16445 CTGAACTGTGTAACTC 72 1173
    882678 N/A N/A 16710 16725 TAGTAGACCACAGTGA 91 1174
    882702 N/A N/A 16950 16965 CACCAGGTTAAACAGG 108 1175
    882726 N/A N/A 17247 17262 TAGTTTAAGGGTTACG 51 1176
    882750 N/A N/A 17554 17569 CTCCAGGGAATGGATA 73 1177
    882774 N/A N/A 17777 17792 GAAAACTCTAACCCTA 91 1178
    882798 N/A N/A 18087 18102 TTATATACTGGTTGGT 51 1179
    882821 N/A N/A 18620 18635 TTAGAGGACAGTGACT 82 1180
    882845 N/A N/A 19018 19033 TGTATAGTTCTCAACC 57 1181
    882868 N/A N/A 19267 19282 TTCCATAGATCAACAT 56 1182
    882905 N/A N/A 12921 12936 CCCTAAGTTTAATTTA 103 1183
  • TABLE 18
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence (% UTC) ID NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 38 195
    881080 16 31 3755 3770 AGATCGAGCGGTGAAA 76 1184
    881104 415 430 6894 6909 TCAAAGCGCACCGCAG 57 1185
    881127 697 712 9187 9202 TGGGACATTGGTACGG 31 1186
    881174 1210 1225 13763 13778 CTGACAAGAACTGCTG 79 1187
    881198 1447 1462 19564 19579 GGCGGATAGATCTGTG 49 1188
    881222 1780 1795 19897 19912 AACCGCTGAACTGAAA 87 1189
    881246 1957 1972 20074 20089 TTAAAGAGCGCATTTC 59 1190
    881270 2048 2063 20165 20180 GACATACCTACAAGCA 50 1191
    881294 2229 2244 20346 20361 AACCGCTGGCAGGTGG 60 1192
    881318 2393 2408 20510 20525 TTAGACATTACTAGAT 55 1193
    881342 2531 2546 20648 20663 AAGTACTTGGACAGAA 46 1194
    881366 2743 2758 20860 20875 CACGAGGAAGCATAGA 44 1195
    881390 2833 2848 20950 20965 ACTTAAGCAAGTGGAG 37 1196
    881414 2917 2932 21034 21049 TGTAGTATGAGAAACG 31 1197
    881438 3059 3074 21176 21191 GCTGAACTGTGTAATG 42 1198
    881462 3345 3360 21462 21477 GTGCAAGATGACTCCA 44 1199
    881486 3435 3450 21552 21567 GTACATGGCAGTGGAG 44 1200
    881510 3523 3538 21640 21655 TGTATACATCACTGCA 37 1201
    881533 3665 3680 21782 21797 AGCTTCTTTGAAGTGC 38 1202
    881557 3921 3936 22038 22053 TTTCATAGCTAGTTCA 44 1203
    881581 4170 4185 22287 22302 GCTTGAGGTTTTCCTA 23 1204
    881600 4312 4327 22429 22444 TCATACCCAATAGTCT 48 1205
    881624 4438 4453 22555 22570 CGCTCAAAGACCAGCT 44 1206
    881648 4559 4574 22676 22691 AAAGTAACTGACACGC 33 1207
    881672 4671 4686 22788 22803 GACCTTAACCAATCCC 36 1208
    881696 4863 4878 22980 22995 GACCTTTACTTCATTC 48 1209
    881720 5157 5172 23274 23289 TCTCAGCAAAACGCAG 73 1210
    881744 5213 5228 23330 23345 ACCAACGACAGCATAG 33 1211
    881768 N/A N/A 18786 18801 TTATATATGACGACTT 65 1212
    881813 N/A N/A 4156 4171 TCGCAGGCAGTTGTGC 120 1213
    881837 N/A N/A 4425 4440 CGCCGGACCCCGGAGC 91 1214
    881860 N/A N/A 4816 4831 CCAAAGGCTCCCGACA 71 1215
    881884 N/A N/A 5065 5080 CCCTTCAGCCACGAGG 92 1216
    881908 N/A N/A 5675 5690 CGTGGAAACGAGAACG 71 1217
    881952 N/A N/A 6229 6244 TCTGAGTGAGCTTGCC 51 1218
    881975 N/A N/A 6541 6556 TGCATAGGCATCCTTC 32 1219
    881998 N/A N/A 7200 7215 ATTAATTCTCCTATGC 85 1220
    882022 N/A N/A 7393 7408 TATTACCATGCATAGT 70 1221
    882046 N/A N/A 7732 7747 AATGCATAACACGGTG 51 1222
    882070 N/A N/A 8154 8169 AGCATATTCCAACAGG 31 1223
    882093 N/A N/A 8417 8432 GTGAAAACACTCATGG 40 1224
    882117 N/A N/A 8606 8621 GCTGAGATAGGAAGCA 81 1225
    8658 8673
    8762 8777
    8866 8881
    8918 8933
    9022 9037
    882140 N/A N/A 9426 9441 AGTAAACTTGGCTGTG 62 1226
    882163 N/A N/A 9710 9725 TGGTAGGTAGGCACCT 65 1227
    882186 N/A N/A 10006 10021 CTTCACTACCTGCAGC 78 1228
    882210 N/A N/A 10190 10205 ATAGAGCCAGAGCAGT 34 1229
    882234 N/A N/A 10372 10387 CACTGAACCATGTTCC 39 1230
    882258 N/A N/A 10677 10692 GCAACTAGCAGGGCAC 47 1231
    882282 N/A N/A 11116 11131 AGTGATGTCAGGTTTT 28 1232
    882306 N/A N/A 11398 11413 AGGCACATCAATGTTT 49 1233
    882330 N/A N/A 11688 11703 TAAAGATGCCAGAGGG 61 1234
    882354 N/A N/A 11999 12014 CACGAGGTTGCCGAGA 36 1235
    882378 N/A N/A 12209 12224 CTGTATCATGCATACC 39 1236
    882401 N/A N/A 12682 12697 CACTGAGGCCTTAATG 66 1237
    882424 N/A N/A 12927 12942 AATGAACCCTAAGTTT 97 1238
    882448 N/A N/A 13290 13305 AACAAAAGGTTCCCGC 60 1239
    882470 N/A N/A 13922 13937 ACAGAAGATCTCTACT 68 1240
    882492 N/A N/A 14205 14220 GTACAGTCCACTCCAC 90 1241
    882515 N/A N/A 14550 14565 GGCACATGAGAAATCA 67 1242
    882538 N/A N/A 14993 15008 AACTGCAGCACCGTGG 55 1243
    882562 N/A N/A 15533 15548 TCACGCAGTGCACCTG 54 1244
    882585 N/A N/A 15826 15841 TGAGAAAGCATGGCTC 60 1245
    882608 N/A N/A 15987 16002 AGCTAACTTACAGGAC 104 1246
    882632 N/A N/A 16208 16223 GTACACAAGACAAATC 79 1247
    882655 N/A N/A 16433 16448 TGCCTGAACTGTGTAA 65 1248
    882679 N/A N/A 16713 16728 AGGTAGTAGACCACAG 41 1249
    882703 N/A N/A 16955 16970 GAACACACCAGGTTAA 102 1250
    882727 N/A N/A 17248 17263 CTAGTTTAAGGGTTAC 73 1251
    882751 N/A N/A 17565 17580 CTACAAAATGCCTCCA 58 1252
    882775 N/A N/A 17778 17793 AGAAAACTCTAACCCT 75 1253
    882799 N/A N/A 18089 18104 GATTATATACTGGTTG 41 1254
    882822 N/A N/A 18623 18638 GACTTAGAGGACAGTG 52 1255
    882846 N/A N/A 19019 19034 CTGTATAGTTCTCAAC 48 1256
    882869 N/A N/A 19283 19298 ATTTTTTGGTTAGTCC 47 1257
    882896 N/A N/A 5796 5811 AACAGAGACGCGGTGA 90 1258
  • TABLE 19
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence (% UTC) ID NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 38 195
    881081 18 33 3757 3772 CAAGATCGAGCGGTGA 62 1259
    881105 416 431 6895 6910 TTCAAAGCGCACCGCA 51 1260
    881128 728 743 9218 9233 TGCCAGTGGTGGCCGC 70 1261
    881175 1211 1226 N/A N/A TCTGACAAGAACTGCT 88 1262
    881199 1448 1463 19565 19580 TGGCGGATAGATCTGT 66 1263
    881223 1784 1799 19901 19916 CCTCAACCGCTGAACT 70 1264
    881247 1958 1973 20075 20090 ATTAAAGAGCGCATTT 87 1265
    881271 2049 2064 20166 20181 AGACATACCTACAAGC 50 1266
    881295 2233 2248 20350 20365 AGGAAACCGCTGGCAG 44 1267
    881319 2395 2410 20512 20527 ACTTAGACATTACTAG 80 1268
    881343 2534 2549 20651 20666 GTTAAGTACTTGGACA 68 1269
    881367 2745 2760 20862 20877 GGCACGAGGAAGCATA 38 1270
    881391 2835 2850 20952 20967 ATACTTAAGCAAGTGG 24 1271
    881415 2918 2933 21035 21050 CTGTAGTATGAGAAAC 55 1272
    881439 3066 3081 21183 21198 GATAAAGGCTGAACTG 33 1273
    881463 3359 3374 21476 21491 CTGCATGAAAGTGTGT 44 1274
    881487 3443 3458 21560 21575 CCTACTGGGTACATGG 37 1275
    881511 3524 3539 21641 21656 ATGTATACATCACTGC 33 1276
    881534 3686 3701 21803 21818 CCTGAGACAGACTTCC 45 1277
    881558 3924 3939 22041 22056 GTATTTCATAGCTAGT 31 1278
    881582 4172 4187 22289 22304 CTGCTTGAGGTTTTCC 26 1279
    881601 4314 4329 22431 22446 GTTCATACCCAATAGT 34 1280
    881625 4449 4464 22566 22581 ATTTATGCCCTCGCTC 74 1281
    881649 4560 4575 22677 22692 AAAAGTAACTGACACG 39 1282
    881673 4675 4690 22792 22807 TAAAGACCTTAACCAA 70 1283
    881697 4909 4924 23026 23041 TTATGCATGTTCCTCA 43 1284
    881721 5164 5179 23281 23296 CTACAGATCTCAGCAA 82 1285
    881745 5216 5231 23333 23348 TATACCAACGACAGCA 51 1286
    881769 N/A N/A 18787 18802 TTTATATATGACGACT 61 1287
    881793 N/A N/A 19455 19470 TAGCAGAGGTTCTACC 74 1288
    881814 N/A N/A 4215 4230 AGGAACGAAGAGCAGG 57 1289
    881838 N/A N/A 4447 4462 GGGATTCCGCGCGCAG 86 1290
    881861 N/A N/A 4818 4833 GCCCAAAGGCTCCCGA 89 1291
    881885 N/A N/A 5362 5377 CCGGAGACCTTGAAGA 91 1292
    881930 N/A N/A 5797 5812 AAACAGAGACGCGGTG 82 1293
    881953 N/A N/A 6241 6256 ACCCACCCAGTGTCTG 82 1294
    881976 N/A N/A 6542 6557 TTGCATAGGCATCCTT 53 1295
    881999 N/A N/A 7203 7218 GTGATTAATTCTCCTA 30 1296
    882023 N/A N/A 7414 7429 CACTTTAAAAGTTGAC 72 1297
    882047 N/A N/A 7733 7748 GAATGCATAACACGGT 39 1298
    882071 N/A N/A 8158 8173 GAGAAGCATATTCCAA 43 1299
    882094 N/A N/A 8431 8446 CTTCATCAGACTAAGT 69 1300
    882118 N/A N/A 8607 8622 GGCTGAGATAGGAAGC 64 1301
    8659 8674
    8763 8778
    8867 8882
    8919 8934
    9023 9038
    882141 N/A N/A 9427 9442 GAGTAAACTTGGCTGT 62 1302
    882164 N/A N/A 9716 9731 ACCCAGTGGTAGGTAG 70 1303
    882187 N/A N/A 10014 10029 GTACACCTCTTCACTA 93 1304
    882211 N/A N/A 10191 10206 CATAGAGCCAGAGCAG 40 1305
    882235 N/A N/A 10448 10463 GCCAAAGAGCCCAATT 67 1306
    882259 N/A N/A 10772 10787 GTCCGACGCACCGCGG 82 1307
    882283 N/A N/A 11122 11137 ACAAGCAGTGATGTCA 27 1308
    882307 N/A N/A 11403 11418 CTCTTAGGCACATCAA 39 1309
    882331 N/A N/A 11689 11704 TTAAAGATGCCAGAGG 72 1310
    882355 N/A N/A 12000 12015 TCACGAGGTTGCCGAG 38 1311
    882379 N/A N/A 12221 12236 CTGATAATTAATCTGT 37 1312
    882402 N/A N/A 12689 12704 GGGTAAGCACTGAGGC 39 1313
    882425 N/A N/A 12990 13005 TTTAAGTCATGTGTCA 50 1314
    882449 N/A N/A 13291 13306 GAACAAAAGGTTCCCG 82 1315
    882471 N/A N/A 13923 13938 GACAGAAGATCTCTAC 83 1316
    882493 N/A N/A 14210 14225 AACCAGTACAGTCCAC 65 1317
    882516 N/A N/A 14551 14566 AGGCACATGAGAAATC 77 1318
    882539 N/A N/A 15020 15035 GGCAATGGAGTCTCGC 50 1319
    882563 N/A N/A 15535 15550 TCTCACGCAGTGCACC 56 1320
    882586 N/A N/A 15837 15852 GCACAATTCTCTGAGA 66 1321
    882609 N/A N/A 16031 16046 TATCAAAGATCTCCAC 75 1322
    882633 N/A N/A 16231 16246 CTTTAGCCCATGCTCC 80 1323
    882656 N/A N/A 16438 16453 CACTATGCCTGAACTG 90 1324
    882680 N/A N/A 16718 16733 TCAAAAGGTAGTAGAC 71 1325
    882704 N/A N/A 16959 16974 CACCGAACACACCAGG 80 1326
    882728 N/A N/A 17287 17302 TCAGACTGTGCTGCTC 64 1327
    882752 N/A N/A 17566 17581 CCTACAAAATGCCTCC 53 1328
    882776 N/A N/A 17808 17823 GTTATCTATGGAAACC 58 1329
    882800 N/A N/A 18090 18105 GGATTATATACTGGTT 23 1330
    882823 N/A N/A 18682 18697 ATGGACCACGCAGCCT 61 1331
    882847 N/A N/A 19026 19041 AGGTAATCTGTATAGT 38 1332
    882870 N/A N/A 19311 19326 TTCATATTTGGAGCCA 34 1333
    882894 N/A N/A 5700 5715 GCCCGGAGGAAGGGCG 106 1334
  • TABLE 20
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID: SEQ ID: SEQ ID: IRF4 SEQ
    Compound I Start 1 Stop 2 Start 2 stop (% ID
    Number Site Site Site Stop Sequence UTC) NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 26 195
    881082 20 35 3759 3774 CCCAAGATCGAGCGGT 72 1335
    881106 417 432 6896 6911 GTTCAAAGCGCACCGC 35 1336
    881129 741 756 9231 9246 ACAAGCTGGGCCTTGC 73 1337
    881152 942 957 13495 13510 GGAGATCCGGCAGCCC 77 1338
    881176 1222 1237 N/A N/A ACGCTTGCAGCTCTGA 52 1339
    881200 1452 1467 19569 19584 GGAATGGCGGATAGAT 67 1340
    881224 1785 1800 19902 19917 TCCTCAACCGCTGAAC 63 1341
    881248 1959 1974 20076 20091 AATTAAAGAGCGCATT 83 1342
    881272 2050 2065 20167 20182 CAGACATACCTACAAG 56 1343
    881296 2234 2249 20351 20366 CAGGAAACCGCTGGCA 26 1344
    881320 2396 2411 20513 20528 TACTTAGACATTACTA 61 1345
    881344 2536 2551 20653 20668 TAGTTAAGTACTTGGA 44 1346
    881368 2746 2761 20863 20878 TGGCACGAGGAAGCAT 54 1347
    881392 2836 2851 20953 20968 TATACTTAAGCAAGTG 53 1348
    881416 2919 2934 21036 21051 CCTGTAGTATGAGAAA 43 1349
    881440 3068 3083 21185 21200 TTGATAAAGGCTGAAC 33 1350
    881464 3364 3379 21481 21496 GAGCACTGCATGAAAG 49 1351
    881488 3444 3459 21561 21576 CCCTACTGGGTACATG 63 1352
    881512 3525 3540 21642 21657 GATGTATACATCACTG 30 1353
    881535 3722 3737 21839 21854 GAGCATCCGCTTGGAG 69 1354
    881559 3926 3941 22043 22058 GAGTATTTCATAGCTA 29 1355
    881583 4173 4188 22290 22305 ACTGCTTGAGGTTTTC 42 1356
    881602 4319 4334 22436 22451 TTTTAGTTCATACCCA 48 1357
    881626 4450 4465 22567 22582 TATTTATGCCCTCGCT 74 1358
    881650 4576 4591 22693 22708 TCTGAATTGTTACTAA 65 1359
    881674 4677 4692 22794 22809 AATAAAGACCTTAACC 89 1360
    881698 4911 4926 23028 23043 TCTTATGCATGTTCCT 38 1361
    881722 5176 5191 23293 23308 AAGCATCCTTTCCTAC 65 1362
    881746 5217 5232 23334 23349 GTATACCAACGACAGC 22 1363
    881770 N/A N/A 18788 18803 TTTTATATATGACGAC 66 1364
    881794 N/A N/A 22820 22835 GAGGACTTCGGGAGAT 77 1365
    881815 N/A N/A 4217 4232 TTAGGAACGAAGAGCA 68 1366
    881839 N/A N/A 4487 4502 GACAAGTGGCGCAGAC 89 1367
    881862 N/A N/A 4853 4868 CTCCTACCCGCCTGCT 85 1368
    881886 N/A N/A 5364 5379 GGCCGGAGACCTTGAA 97 1369
    881909 N/A N/A 5712 5727 CGGCAGACGGGAGCCC 88 1370
    881931 N/A N/A 5798 5813 GAAACAGAGACGCGGT 99 1371
    881954 N/A N/A 6265 6280 GCGGAGGTTCCTTGAG 56 1372
    882000 N/A N/A 7211 7226 CATACAGTGTGATTAA 47 1373
    882024 N/A N/A 7424 7439 GACCATGTTACACTTT 50 1374
    882048 N/A N/A 7736 7751 TTAGAATGCATAACAC 56 1375
    882072 N/A N/A 8159 8174 TGAGAAGCATATTCCA 28 1376
    882095 N/A N/A 8443 8458 CTGGAGTGAACCCTTC 44 1377
    882119 N/A N/A 8701 8716 AGAAGCACTGGCATCG 63 1378
    8805 8820
    8961 8976
    882142 N/A N/A 9430 9445 TGAGAGTAAACTTGGC 35 1379
    882165 N/A N/A 9742 9757 ATCCACAATCAGCAAG 49 1380
    882188 N/A N/A 10016 10031 TGGTACACCTCTTCAC 68 1381
    882212 N/A N/A 10192 10207 CCATAGAGCCAGAGCA 36 1382
    882236 N/A N/A 10464 10479 GTCTACTTGAGTCTGT 49 1383
    882260 N/A N/A 10780 10795 GACAGAGAGTCCGACG 101 1384
    882284 N/A N/A 11123 11138 CACAAGCAGTGATGTC 40 1385
    882308 N/A N/A 11405 11420 TACTCTTAGGCACATC 41 1386
    882332 N/A N/A 11723 11738 TCAGAATTTAGTTAGT 67 1387
    882356 N/A N/A 12001 12016 ATCACGAGGTTGCCGA 40 1388
    882380 N/A N/A 12223 12238 GGCTGATAATTAATCT 53 1389
    882403 N/A N/A 12695 12710 ATTAAAGGGTAAGCAC 68 1390
    882426 N/A N/A 13007 13022 TGATAGTGGTGATGTC 46 1391
    882450 N/A N/A 13292 13307 GGAACAAAAGGTTCCC 88 1392
    882472 N/A N/A 13956 13971 TCTGATCCGGACTCTC 59 1393
    882494 N/A N/A 14213 14228 CAAAACCAGTACAGTC 51 1394
    882517 N/A N/A 14622 14637 CCAGAGCACACAGACG 64 1395
    882540 N/A N/A 15021 15036 GGGCAATGGAGTCTCG 76 1396
    882564 N/A N/A 15538 15553 GTCTCTCACGCAGTGC 50 1397
    882587 N/A N/A 15838 15853 GGCACAATTCTCTGAG 57 1398
    882610 N/A N/A 16033 16048 GATATCAAAGATCTCC 43 1399
    882634 N/A N/A 16254 16269 AAAGACAAGTGCCCAT 76 1400
    882657 N/A N/A 16441 16456 TGTCACTATGCCTGAA 73 1401
    882681 N/A N/A 16726 16741 ACGAAGATTCAAAAGG 64 1402
    882705 N/A N/A 16962 16977 CATCACCGAACACACC 76 1403
    882729 N/A N/A 17289 17304 CCTCAGACTGTGCTGC 70 1404
    882753 N/A N/A 17567 17582 ACCTACAAAATGCCTC 58 1405
    882777 N/A N/A 17826 17841 GGCAAATTAATGCTTC 24 1406
    882801 N/A N/A 18096 18111 TCTATGGGATTATATA 74 1407
    882824 N/A N/A 18684 18699 TTATGGACCACGCAGC 69 1408
    882848 N/A N/A 19030 19045 TTCTAGGTAATCTGTA 62 1409
    882871 N/A N/A 19312 19327 TTTCATATTTGGAGCC 25 1410
    882899 N/A N/A 6633 6648 AGTAGCTGGGCCCTCG 38 1411
  • TABLE 21
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID: SEQ ID: SEQ ID: IRF4 SEQ
    Compound I Start 1 Stop 2 Start 2 stop (% ID
    Number Site Site Site Stop Sequence UTC) NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 31 195
    668815 436 451 6915 6930 CCTCAAAGTCATTGCT 79 1412
    881083 21 36 3760 3775 TCCCAAGATCGAGCGG 84 1413
    881130 743 758 9233 9248 TCACAAGCTGGGCCTT 70 1414
    881153 946 961 13499 13514 CATGGGAGATCCGGCA 59 1415
    881177 1235 1250 17028 17043 CCGTGGTGAGCAAACG 68 1416
    881201 1453 1468 19570 19585 AGGAATGGCGGATAGA 62 1417
    881225 1793 1808 19910 19925 CGCAATTCTCCTCAAC 62 1418
    881249 1960 1975 20077 20092 AAATTAAAGAGCGCAT 87 1419
    881273 2054 2069 20171 20186 GGCACAGACATACCTA 52 1420
    881297 2237 2252 20354 20369 CACCAGGAAACCGCTG 85 1421
    881321 2399 2414 20516 20531 CATTACTTAGACATTA 81 1422
    881345 2537 2552 20654 20669 ATAGTTAAGTACTTGG 52 1423
    881369 2752 2767 20869 20884 TATAATTGGCACGAGG 59 1424
    881393 2837 2852 20954 20969 GTATACTTAAGCAAGT 58 1425
    881417 2921 2936 21038 21053 ATCCTGTAGTATGAGA 55 1426
    881441 3069 3084 21186 21201 CTTGATAAAGGCTGAA 40 1427
    881465 3372 3387 21489 21504 GCTACAAAGAGCACTG 37 1428
    881489 3449 3464 21566 21581 TCAAACCCTACTGGGT 92 1429
    881513 3532 3547 21649 21664 TCTATAAGATGTATAC 74 1430
    881536 3726 3741 21843 21858 AATGGAGCATCCGCTT 107 1431
    881560 3945 3960 22062 22077 TGCTAGGATTCCTAAC 74 1432
    881584 4174 4189 22291 22306 TACTGCTTGAGGTTTT 50 1433
    881603 4320 4335 22437 22452 TTTTTAGTTCATACCC 59 1434
    881627 4451 4466 22568 22583 GTATTTATGCCCTCGC 47 1435
    881651 4577 4592 22694 22709 ATCTGAATTGTTACTA 88 1436
    881675 4732 4747 22849 22864 CACCATTCAGACAGAT 167 1437
    881699 4918 4933 23035 23050 CTACATTTCTTATGCA 61 1438
    881723 5180 5195 23297 23312 TGTGAAGCATCCTTTC 55 1439
    881747 5218 5233 23335 23350 TGTATACCAACGACAG 42 1440
    881771 N/A N/A 18804 18819 GATATTAGAGACTGTA 49 1441
    881795 N/A N/A 22823 22838 ACAGAGGACTTCGGGA 136 1442
    881816 N/A N/A 4218 4233 CTTAGGAACGAAGAGC 93 1443
    881840 N/A N/A 4491 4506 AAACGACAAGTGGCGC 79 1444
    881863 N/A N/A 4860 4875 GCGAAGGCTCCTACCC 115 1445
    881887 N/A N/A 5369 5384 CCCGAGGCCGGAGACC 94 1446
    881910 N/A N/A 5720 5735 GACGGAGGCGGCAGAC 143 1447
    881932 N/A N/A 5815 5830 GAAAAGCAGCGAAAAG 98 1448
    881955 N/A N/A 6278 6293 GGTAGAGTGAGATGCG 42 1449
    881977 N/A N/A 6663 6678 GTTCTAGGGTCCTCCT 50 1450
    882001 N/A N/A 7213 7228 GGCATACAGTGTGATT 75 1451
    882025 N/A N/A 7428 7443 AGCTGACCATGTTACA 119 1452
    882049 N/A N/A 7737 7752 CTTAGAATGCATAACA 74 1453
    882073 N/A N/A 8213 8228 GGCACTACTTCCAAAA 69 1454
    882096 N/A N/A 8452 8467 CCGAAAAGACTGGAGT 43 1455
    882120 N/A N/A 8702 8717 AAGAAGCACTGGCATC 77 1456
    8806 8821
    8962 8977
    882143 N/A N/A 9432 9447 CCTGAGAGTAAACTTG 82 1457
    882166 N/A N/A 9745 9760 CTAATCCACAATCAGC 55 1458
    882189 N/A N/A 10024 10039 TTAAAGAGTGGTACAC 94 1459
    882213 N/A N/A 10194 10209 TTCCATAGAGCCAGAG 63 1460
    882237 N/A N/A 10497 10512 CAAAGCGGGTTCACAA 84 1461
    882261 N/A N/A 10781 10796 AGACAGAGAGTCCGAC 93 1462
    882285 N/A N/A 11126 11141 AACCACAAGCAGTGAT 83 1463
    882309 N/A N/A 11409 11424 GTATTACTCTTAGGCA 36 1464
    882333 N/A N/A 11750 11765 GCCACAACTCTCGCCT 75 1465
    882357 N/A N/A 12004 12019 GAAATCACGAGGTTGC 38 1466
    882381 N/A N/A 12241 12256 TCTAATAAATGTGCTC 56 1467
    882404 N/A N/A 12698 12713 CACATTAAAGGGTAAG 101 1468
    882427 N/A N/A 13049 13064 ACTATTAAGAACTTGC 79 1469
    882451 N/A N/A 13293 13308 GGGAACAAAAGGTTCC 111 1470
    882473 N/A N/A 13957 13972 ATCTGATCCGGACTCT 91 1471
    882495 N/A N/A 14214 14229 GCAAAACCAGTACAGT 42 1472
    882518 N/A N/A 14630 14645 CAACAGTGCCAGAGCA 89 1473
    882541 N/A N/A 15070 15085 TCCTATGGTCAGCCTC 52 1474
    882565 N/A N/A 15590 15605 CGCAAGTCTACAGCCC 41 1475
    882588 N/A N/A 15839 15854 TGGCACAATTCTCTGA 87 1476
    882611 N/A N/A 16042 16057 GAATAGGAAGATATCA 94 1477
    882635 N/A N/A 16256 16271 GGAAAGACAAGTGCCC 46 1478
    882658 N/A N/A 16447 16462 TCCCACTGTCACTATG 85 1479
    882682 N/A N/A 16727 16742 CACGAAGATTCAAAAG 90 1480
    882706 N/A N/A 16971 16986 AGAAACCCTCATCACC 105 1481
    882730 N/A N/A 17330 17345 CTTTGATGAGCAGATC 88 1482
    882754 N/A N/A 17570 17585 GAGACCTACAAAATGC 89 1483
    882778 N/A N/A 17856 17871 GTCTTAAGGGTTCAAG 51 1484
    882802 N/A N/A 18097 18112 GTCTATGGGATTATAT 79 1485
    882825 N/A N/A 18685 18700 TTTATGGACCACGCAG 62 1486
    882849 N/A N/A 19033 19048 GATTTCTAGGTAATCT 69 1487
    882872 N/A N/A 19337 19352 TTACATCCTAGAACAC 97 1488
  • TABLE 22
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID: SEQ ID: SEQ ID: IRF4 SEQ
    Compound I Start 1 Stop 2 Start 2 stop (% ID
    Number Site Site Site Stop Sequence UTC) NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 35 195
    669124 3537 3552 21654 21669 TTGCATCTATAAGATG 69 1489
    881084 44 59 3783 3798 TCGGAGCTGAGGGCAG 82 1490
    881107 448 463 6927 6942 GCTCAACCAGTTCCTC 62 1491
    881131 754 769 N/A N/A GGCAACCATTTTCACA 117 1492
    881154 949 964 13502 13517 GTCCATGGGAGATCCG 48 1493
    881178 1245 1260 17038 17053 CAGGGAGCGGCCGTGG 83 1494
    881202 1454 1469 19571 19586 GAGGAATGGCGGATAG 69 1495
    881226 1794 1809 19911 19926 CCGCAATTCTCCTCAA 80 1496
    881250 1961 1976 20078 20093 CAAATTAAAGAGCGCA 43 1497
    881274 2055 2070 20172 20187 TGGCACAGACATACCT 62 1498
    881298 2240 2255 20357 20372 CCACACCAGGAAACCG 86 1499
    881322 2400 2415 20517 20532 CCATTACTTAGACATT 36 1500
    881346 2538 2553 20655 20670 GATAGTTAAGTACTTG 51 1501
    881370 2756 2771 20873 20888 AAACTATAATTGGCAC 70 1502
    881394 2838 2853 20955 20970 GGTATACTTAAGCAAG 32 1503
    881418 2927 2942 21044 21059 GTAAATATCCTGTAGT 67 1504
    881442 3070 3085 21187 21202 GCTTGATAAAGGCTGA 27 1505
    881466 3373 3388 21490 21505 AGCTACAAAGAGCACT 67 1506
    881490 3450 3465 21567 21582 GTCAAACCCTACTGGG 69 1507
    881537 3729 3744 21846 21861 TGAAATGGAGCATCCG 91 1508
    881561 3951 3966 22068 22083 GACAAGTGCTAGGATT 39 1509
    881585 4176 4191 22293 22308 ATTACTGCTTGAGGTT 38 1510
    881604 4321 4336 22438 22453 CTTTTTAGTTCATACC 63 1511
    881628 4452 4467 22569 22584 TGTATTTATGCCCTCG 56 1512
    881652 4580 4595 22697 22712 TGGATCTGAATTGTTA 45 1513
    881676 4735 4750 22852 22867 ACGCACCATTCAGACA 102 1514
    881700 4972 4987 23089 23104 GGAGGAGGGTTGGCCT 99 1515
    881724 5181 5196 23298 23313 TTGTGAAGCATCCTTT 37 1516
    881748 5219 5234 23336 23351 ATGTATACCAACGACA 37 1517
    881772 N/A N/A 18805 18820 TGATATTAGAGACTGT 40 1518
    881796 N/A N/A 22825 22840 CCACAGAGGACTTCGG 73 1519
    881817 N/A N/A 4220 4235 CCCTTAGGAACGAAGA 106 1520
    881841 N/A N/A 4494 4509 TGCAAACGACAAGTGG 79 1521
    881864 N/A N/A 4861 4876 CGCGAAGGCTCCTACC 141 1522
    881888 N/A N/A 5370 5385 TCCCGAGGCCGGAGAC 127 1523
    881911 N/A N/A 5723 5738 ACGGACGGAGGCGGCA 89 1524
    881956 N/A N/A 6279 6294 CGGTAGAGTGAGATGC 46 1525
    881978 N/A N/A 6677 6692 CATCGAACTCCTGAGT 69 1526
    882002 N/A N/A 7218 7233 ATTGAGGCATACAGTG 70 1527
    882026 N/A N/A 7437 7452 AAACACCTCAGCTGAC 84 1528
    882050 N/A N/A 7784 7799 GACCTAACTAAATGTC 118 1529
    882074 N/A N/A 8218 8233 GATAAGGCACTACTTC 53 1530
    882097 N/A N/A 8463 8478 CATTTTATCATCCGAA 45 1531
    882121 N/A N/A 8753 8768 GGAAGCACTGGCATTG 51 1532
    8857 8872
    8909 8924
    882144 N/A N/A 9442 9457 TAGCATGGATCCTGAG 100 1533
    882167 N/A N/A 9746 9761 TCTAATCCACAATCAG 59 1534
    882190 N/A N/A 10025 10040 ATTAAAGAGTGGTACA 107 1535
    882214 N/A N/A 10198 10213 CTAATTCCATAGAGCC 20 1536
    882238 N/A N/A 10500 10515 TCACAAAGCGGGTTCA 77 1537
    882262 N/A N/A 10785 10800 GTCTAGACAGAGAGTC 98 1538
    882286 N/A N/A 11151 11166 AGCCAGTGGCTGAAAC 79 1539
    882310 N/A N/A 11411 11426 GTGTATTACTCTTAGG 14 1540
    882334 N/A N/A 11751 11766 TGCCACAACTCTCGCC 69 1541
    882358 N/A N/A 12005 12020 AGAAATCACGAGGTTG 36 1542
    882382 N/A N/A 12260 12275 TCAATGGGAATCACAG 60 1543
    882405 N/A N/A 12699 12714 ACACATTAAAGGGTAA 89 1544
    882428 N/A N/A 13050 13065 CACTATTAAGAACTTG 67 1545
    882452 N/A N/A 13309 13324 CCCACATGTCCCGTGG 95 1546
    882474 N/A N/A 13995 14010 TTGCAAGAGAACAGCC 61 1547
    882496 N/A N/A 14215 14230 TGCAAAACCAGTACAG 72 1548
    882519 N/A N/A 14639 14654 AGCACATGTCAACAGT 69 1549
    882542 N/A N/A 15091 15106 AACCAGCACAGTTCTC 118 1550
    882566 N/A N/A 15591 15606 GCGCAAGTCTACAGCC 120 1551
    882589 N/A N/A 15854 15869 ATCAGAATGGCGAGTT 53 1552
    882612 N/A N/A 16046 16061 ACCTGAATAGGAAGAT 69 1553
    882636 N/A N/A 16258 16273 TTGGAAAGACAAGTGC 85 1554
    882659 N/A N/A 16464 16479 AGCCATCGGCAGCTGA 86 1555
    882683 N/A N/A 16733 16748 TGGACCCACGAAGATT 62 1556
    882707 N/A N/A 16972 16987 CAGAAACCCTCATCAC 96 1557
    882731 N/A N/A 17367 17382 AAAGAGGCACCCTCCT 138 1558
    882755 N/A N/A 17588 17603 TGCTAGGACACAGCTG 57 1559
    882779 N/A N/A 17862 17877 TCAAAAGTCTTAAGGG 93 1560
    882803 N/A N/A 18111 18126 GAGAAAACTCCTGAGT 95 1561
    882826 N/A N/A 18686 18701 TTTTATGGACCACGCA 69 1562
    882850 N/A N/A 19079 19094 CACAACTGCAGTTTGA 86 1563
    882873 N/A N/A 19343 19358 CCAAAGTTACATCCTA 61 1564
    882897 N/A N/A 5887 5902 CCGCAGAGAGCTAGCA 106 1565
  • TABLE 23
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID: SEQ ID: SEQ ID:
    Compound 1 Start 1 Stop 2 Start 2 Stop IRF4 (% SEQ
    Number Site Site Site Site Sequence UTC) ID NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 48 195
    881085 49 64 3788 3803 TGGACTCGGAGCTGAG 76 1566
    881108 462 477 6941 6956 GTCCAGCTGGCTCCGC 47 1567
    881132 762 777 N/A N/A TGTCACCTGGCAACCA 91 1568
    881155 987 1002 13540 13555 GAACAGGACCTGGTCC 75 1569
    881203 1455 1470 19572 19587 AGAGGAATGGCGGATA 58 1570
    881251 1962 1977 20079 20094 ACAAATTAAAGAGCGC 36 1571
    881275 2078 2093 20195 20210 TTACATCTTACTTCCC 58 1572
    881299 2306 2321 20423 20438 ACTAACTGGCTTCCAG 69 1573
    881323 2401 2416 20518 20533 ACCATTACTTAGACAT 35 1574
    881347 2539 2554 20656 20671 AGATAGTTAAGTACTT 89 1575
    881371 2758 2773 20875 20890 TCAAACTATAATTGGC 26 1576
    881395 2839 2854 20956 20971 AGGTATACTTAAGCAA 32 1577
    881419 2929 2944 21046 21061 TAGTAAATATCCTGTA 58 1578
    881443 3071 3086 21188 21203 AGCTTGATAAAGGCTG 64 1579
    881467 3376 3391 21493 21508 GTTAGCTACAAAGAGC 59 1580
    881491 3451 3466 21568 21583 TGTCAAACCCTACTGG 77 1581
    881514 3549 3564 21666 21681 CCCCAAAATACTTTGC 0 1582
    881538 3730 3745 21847 21862 TTGAAATGGAGCATCC 78 1583
    881562 3952 3967 22069 22084 AGACAAGTGCTAGGAT 44 1584
    881586 4186 4201 22303 22318 GGAGATATTAATTACT 50 1585
    881605 4369 4384 22486 22501 GCTCATTTCACTGTAG 36 1586
    881629 4453 4468 22570 22585 CTGTATTTATGCCCTC 40 1587
    881653 4584 4599 22701 22716 ACACTGGATCTGAATT 54 1588
    881677 4742 4757 22859 22874 AGCCTTCACGCACCAT 70 1589
    881701 4976 4991 23093 23108 CATTGGAGGAGGGTTG 102 1590
    881725 5183 5198 23300 23315 GTTTGTGAAGCATCCT 35 1591
    881749 5220 5235 23337 23352 GATGTATACCAACGAC 32 1592
    881773 N/A N/A 18806 18821 ATGATATTAGAGACTG 26 1593
    881797 N/A N/A 3804 3819 AGCCCTTACCTCGCCC 75 1594
    881818 N/A N/A 4239 4254 GGCCGCCGTGAGCTTG 97 1595
    881865 N/A N/A 4862 4877 CCGCGAAGGCTCCTAC 86 1596
    881912 N/A N/A 5724 5739 CACGGACGGAGGCGGC 82 1597
    881933 N/A N/A 5894 5909 GGAGTACCCGCAGAGA 75 1598
    881957 N/A N/A 6282 6297 AACCGGTAGAGTGAGA 94 1599
    881979 N/A N/A 6682 6697 CGCAGCATCGAACTCC 67 1600
    882003 N/A N/A 7219 7234 CATTGAGGCATACAGT 45 1601
    882027 N/A N/A 7439 7454 ATAAACACCTCAGCTG 79 1602
    882051 N/A N/A 7791 7806 AGGAACTGACCTAACT 69 1603
    882075 N/A N/A 8219 8234 TGATAAGGCACTACTT 65 1604
    882098 N/A N/A 8464 8479 GCATTTTATCATCCGA 37 1605
    882122 N/A N/A 8754 8769 AGGAAGCACTGGCATT 41 1606
    8858 8873
    8910 8925
    882145 N/A N/A 9458 9473 CACGAAGGGCAGTGCC 83 1607
    882168 N/A N/A 9747 9762 ATCTAATCCACAATCA 70 1608
    882191 N/A N/A 10026 10041 CATTAAAGAGTGGTAC 103 1609
    882215 N/A N/A 10199 10214 ACTAATTCCATAGAGC 21 1610
    882239 N/A N/A 10519 10534 TGACATGCTTTGTCCT 41 1611
    882263 N/A N/A 10795 10810 ATCAGATGATGTCTAG 103 1612
    882287 N/A N/A 11160 11175 CTCCATTCAAGCCAGT 42 1613
    882311 N/A N/A 11446 11461 GCAAGCTATATTAAAG 29 1614
    882335 N/A N/A 11757 11772 CAAAAGTGCCACAACT 90 1615
    882359 N/A N/A 12008 12023 ATCAGAAATCACGAGG 29 1616
    882383 N/A N/A 12261 12276 ATCAATGGGAATCACA 10 1617
    882406 N/A N/A 12701 12716 ACACACATTAAAGGGT 57 1618
    882429 N/A N/A 13055 13070 AGCATCACTATTAAGA 28 1619
    882453 N/A N/A 13323 13338 TGGAACTCTAGTGTCC 98 1620
    882475 N/A N/A 14002 14017 ACCAGAATTGCAAGAG 40 1621
    882497 N/A N/A 14216 14231 GTGCAAAACCAGTACA 67 1622
    882520 N/A N/A 14640 14655 GAGCACATGTCAACAG 60 1623
    882543 N/A N/A 15112 15127 TCACTTGCCGCCGCCT 51 1624
    882567 N/A N/A 15600 15615 GTTCTAGTCGCGCAAG 73 1625
    882590 N/A N/A 15855 15870 AATCAGAATGGCGAGT 61 1626
    882613 N/A N/A 16052 16067 GTGCAGACCTGAATAG 86 1627
    882637 N/A N/A 16269 16284 CTGGAACATTGTTGGA 54 1628
    882660 N/A N/A 16501 16516 CAGAAAATATGTAACG 78 1629
    882684 N/A N/A 16736 16751 CATTGGACCCACGAAG 72 1630
    882708 N/A N/A 16975 16990 GTTCAGAAACCCTCAT 87 1631
    882732 N/A N/A 17368 17383 GAAAGAGGCACCCTCC 81 1632
    882756 N/A N/A 17597 17612 TAAAAGAGGTGCTAGG 73 1633
    882780 N/A N/A 17889 17904 GTATGTAGCAATGTGA 79 1634
    882804 N/A N/A 18126 18141 CTGGAGAGAACTCATG 62 1635
    882827 N/A N/A 18687 18702 ATTTTATGGACCACGC 51 1636
    882851 N/A N/A 19080 19095 CCACAACTGCAGTTTG 77 1637
    882874 N/A N/A 19346 19361 AGCCCAAAGTTACATC 58 1638
    882893 N/A N/A 4508 4523 CACTAAGTGGGCTCTG 59 1639
  • TABLE 24
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID: SEQ ID: SEQ ID: IRF4 SEQ
    Compound 1 Start 1 Stop 2 Start 2 Stop (% ID
    Number Site Site Site Site Sequence UTC) NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 23 195
    881086 149 164 5176 5191 CCGAACTCTCCGCCTC 64 1640
    881133 774 789 10839 10854 ATAAAAGGTTCCTGTC 16 1641
    881180 1256 1271 17049 17064 TGGAATCTTGGCAGGG 60 1642
    881204 1457 1472 19574 19589 ATAGAGGAATGGCGGA 35 1643
    881228 1828 1843 19945 19960 AATCAGATGTCACTGA 97 1644
    881252 1973 1988 20090 20105 CCTAATCTACAACAAA 85 1645
    881276 2124 2139 20241 20256 CCTACATACATTAATA 107 1646
    881300 2307 2322 20424 20439 TACTAACTGGCTTCCA 72 1647
    881324 2402 2417 20519 20534 AACCATTACTTAGACA 55 1648
    881348 2540 2555 20657 20672 CAGATAGTTAAGTACT 56 1649
    881372 2760 2775 20877 20892 TGTCAAACTATAATTG 85 1650
    881396 2840 2855 20957 20972 TAGGTATACTTAAGCA 21 1651
    881420 2933 2948 21050 21065 GTAATAGTAAATATCC 39 1652
    881444 3076 3091 21193 21208 CACTAAGCTTGATAAA 111 1653
    881468 3377 3392 21494 21509 TGTTAGCTACAAAGAG 53 1654
    881492 3456 3471 21573 21588 TGAAATGTCAAACCCT 46 1655
    881515 3559 3574 21676 21691 GGATAATATACCCCAA 36 1656
    881539 3731 3746 21848 21863 ATTGAAATGGAGCATC 101 1657
    881587 4187 4202 22304 22319 AGGAGATATTAATTAC 43 1658
    881606 4378 4393 22495 22510 GTAAGGGCTGCTCATT 48 1659
    881630 4459 4474 22576 22591 GGCTAGCTGTATTTAT 63 1660
    881654 4586 4601 22703 22718 TTACACTGGATCTGAA 62 1661
    881678 4755 4770 22872 22887 TGTAAGGTCTGAGAGC 75 1662
    881702 4978 4993 23095 23110 TCCATTGGAGGAGGGT 67 1663
    881726 5184 5199 23301 23316 AGTTTGTGAAGCATCC 31 1664
    881750 5222 5237 23339 23354 ATGATGTATACCAACG 14 1665
    881774 N/A N/A 18807 18822 CATGATATTAGAGACT 44 1666
    881798 N/A N/A 3865 3880 CTGGTTCGCGCTCCGG 93 1667
    881819 N/A N/A 4244 4259 CCGGAGGCCGCCGTGA 87 1668
    881842 N/A N/A 4510 4525 CGCACTAAGTGGGCTC 86 1669
    881866 N/A N/A 4892 4907 GCACAGCCGTCCGCCT 84 1670
    881890 N/A N/A 5492 5507 CGCCACCTGATGCCTC 70 1671
    881913 N/A N/A 5726 5741 CCCACGGACGGAGGCG 109 1672
    881934 N/A N/A 5896 5911 TGGGAGTACCCGCAGA 74 1673
    881958 N/A N/A 6284 6299 ATAACCGGTAGAGTGA 50 1674
    881980 N/A N/A 6683 6698 CCGCAGCATCGAACTC 58 1675
    882028 N/A N/A 7481 7496 GGTCAGAATCTTGAAA 91 1676
    882052 N/A N/A 7795 7810 AAACAGGAACTGACCT 80 1677
    882076 N/A N/A 8220 8235 ATGATAAGGCACTACT 87 1678
    882099 N/A N/A 8465 8480 AGCATTTTATCATCCG 19 1679
    882123 N/A N/A 8781 8796 TTAAAGGAGTGCAGGA 84 1680
    882146 N/A N/A 9460 9475 CCCACGAAGGGCAGTG 65 1681
    882169 N/A N/A 9751 9766 CCACATCTAATCCACA 33 1682
    882192 N/A N/A 10049 10064 GTGAACATGCCACTCA 38 1683
    882216 N/A N/A 10200 10215 TACTAATTCCATAGAG 74 1684
    882240 N/A N/A 10520 10535 ATGACATGCTTTGTCC 54 1685
    882264 N/A N/A 10939 10954 AGCAAACCCTGCACTC 92 1686
    882288 N/A N/A 11215 11230 GGTAAAGGCACATTCC 53 1687
    882312 N/A N/A 11448 11463 TTGCAAGCTATATTAA 66 1688
    882336 N/A N/A 11790 11805 TGGTAGGTCAAACTCC 113 1689
    882360 N/A N/A 12009 12024 CATCAGAAATCACGAG 45 1690
    882384 N/A N/A 12283 12298 GGTAACTGTATGGAAC 24 1691
    882407 N/A N/A 12757 12772 GAATTAGGTGCTTAAT 41 1692
    882430 N/A N/A 13060 13075 TATAGAGCATCACTAT 59 1693
    882454 N/A N/A 13324 13339 GTGGAACTCTAGTGTC 88 1694
    882476 N/A N/A 14021 14036 TAAGAGGCGACTGCTG 145 1695
    882498 N/A N/A 14233 14248 CTCCTATAACTTCTCC 67 1696
    882521 N/A N/A 14643 14658 TACGAGCACATGTCAA 64 1697
    882544 N/A N/A 15146 15161 TAGAATGAGAGGTGTC 71 1698
    882568 N/A N/A 15609 15624 TAATAGTAAGTTCTAG 100 1699
    882591 N/A N/A 15860 15875 AGGCTAATCAGAATGG 58 1700
    882614 N/A N/A 16099 16114 TCAGATACACACCCTC 63 1701
    882638 N/A N/A 16276 16291 AAACGGACTGGAACAT 93 1702
    882661 N/A N/A 16516 16531 GTAACTCAGGCACCAC 53 1703
    882685 N/A N/A 16758 16773 GCTAAAGAACACTGCT 97 1704
    882709 N/A N/A 16981 16996 GACCATGTTCAGAAAC 4 1705
    882733 N/A N/A 17369 17384 GGAAAGAGGCACCCTC 72 1706
    882757 N/A N/A 17640 17655 TATCATATGCCCAATA 68 1707
    882781 N/A N/A 17894 17909 TGCAAGTATGTAGCAA 97 1708
    882805 N/A N/A 18131 18146 AATCACTGGAGAGAAC 71 1709
    882828 N/A N/A 18688 18703 CATTTTATGGACCACG 38 1710
    882852 N/A N/A 19099 19114 GGCCAATGATTTTGTT 94 1711
    882875 N/A N/A 19350 19365 GTAAAGCCCAAAGTTA 73 1712
  • Example 6: Effect of 3-10-3 cEt Gapmers with Phosphorothioate Internucleoside Linkages on Human IRF4 In Vitro, Single Dose
  • Modified oligonucleotides complementary to a human IRF4 nucleic acid were designed and tested for their effect on IRF4 mRNA in vitro.
  • Cultured SK-MEL-28 cells at a density of 20,000 cells per well were transfected using electroporation with 4,000 nM concentration of modified oligonucleotide or no modified oligonucleotide for untreated controls. After approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by quantitative real-time PCR. Human primer probe set RTS3114 (described hereinabove in Example 1) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN®. Results are presented in the table below as percent control of the amount of IRF4 mRNA, relative to untreated control (UTC) cells.
  • The modified oligonucleotides in Tables 25 through 36 are 3-10-3 cEt gapmers. The gapmers are 16 nucleobases in length, wherein the central gap segment comprises ten 2′-deoxynucleosides and is flanked by wing segments on both the 5′ end and on the 3′ end comprising three cEt nucleosides. The sugar motif for the gapmers is (from 5′ to 3′): kkkddddddddddkkk; wherein ‘d’ represents a 2′-deoxyribose sugar and ‘k’ represents a cEt modified sugar. Each internucleoside linkage is a phosphorothioate internucleoside linkage and each cytosine residue is a 5-methylcytosine. “Start Site” indicates the 5′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence. “Stop Site” indicates the 3′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Each modified oligonucleotide listed in Tables 25 through 36 below is complementary to human IRF4 nucleic acid sequences SEQ ID NO: 1 or SEQ ID NO: 2, as indicated. ‘N/A’ indicates that the modified oligonucleotide is not complementary to that particular nucleic acid sequence with 100% complementarity. As shown below, modified oligonucleotides complementary to human IRF4 reduced the amount of human IRF4 mRNA.
  • TABLE 25
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID: SEQ ID: SEQ ID: IRF4
    Compound 1 Start 1 Stop 2 Start 2 Stop (% SEQ
    Number Site Site Site Site Sequence UTC) ID NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 44 195
    881087 151 166 5178 5193 TGCCGAACTCTCCGCC 57 1713
    881110 482 497 6961 6976 ACTTTGTACGGGTCTG 61 1714
    881134 778 793 10843 10858 AAGCATAAAAGGTTCC 72 1715
    881157 1059 1074 13612 13627 GACCACGCCCCTCTCC 45 1716
    881181 1263 1278 17056 17071 AGTCACCTGGAATCTT 53 1717
    881205 1458 1473 19575 19590 AATAGAGGAATGGCGG 47 1718
    881229 1831 1846 19948 19963 GCCAATCAGATGTCAC 54 1719
    881253 1974 1989 20091 20106 ACCTAATCTACAACAA 83 1720
    881277 2128 2143 20245 20260 AGCTCCTACATACATT 56 1721
    881301 2309 2324 20426 20441 TTTACTAACTGGCTTC 55 1722
    881325 2432 2447 20549 20564 GGTCAAAAAGATGCAG 49 1723
    881349 2541 2556 20658 20673 ACAGATAGTTAAGTAC 65 1724
    881373 2770 2785 20887 20902 TTTAAGGCCCTGTCAA 117 1725
    881397 2842 2857 20959 20974 GATAGGTATACTTAAG 49 1726
    881421 2938 2953 21055 21070 TGGGAGTAATAGTAAA 84 1727
    881445 3077 3092 21194 21209 TCACTAAGCTTGATAA 63 1728
    881469 3383 3398 21500 21515 CTTCACTGTTAGCTAC 49 1729
    881493 3468 3483 21585 21600 TTGCATGGCTAATGAA 58 1730
    881516 3560 3575 21677 21692 AGGATAATATACCCCA 26 1731
    881540 3733 3748 21850 21865 CAATTGAAATGGAGCA 74 1732
    881564 3956 3971 22073 22088 CCTGAGACAAGTGCTA 57 1733
    881588 4200 4215 22317 22332 TCTATAGTGTTCCAGG 20 1734
    881607 4380 4395 22497 22512 CTGTAAGGGCTGCTCA 44 1735
    881631 4482 4497 22599 22614 TCCCAGAGTTGTTCCA 74 1736
    881655 4587 4602 22704 22719 TTTACACTGGATCTGA 75 1737
    881679 4756 4771 22873 22888 GTGTAAGGTCTGAGAG 84 1738
    881703 4979 4994 23096 23111 TTCCATTGGAGGAGGG 72 1739
    881727 5185 5200 23302 23317 CAGTTTGTGAAGCATC 22 1740
    881751 5223 5238 23340 23355 CATGATGTATACCAAC 49 1741
    881775 N/A N/A 18808 18823 TCATGATATTAGAGAC 65 1742
    881799 N/A N/A 3874 3889 GTCGAACCTCTGGTTC 110 1743
    881820 N/A N/A 4246 4261 CGCCGGAGGCCGCCGT 97 1744
    881843 N/A N/A 4511 4526 GCGCACTAAGTGGGCT 110 1745
    881867 N/A N/A 4893 4908 GGCACAGCCGTCCGCC 89 1746
    881891 N/A N/A 5535 5550 CTGAGAGCCGAGGCCT 117 1747
    881914 N/A N/A 5727 5742 ACCCACGGACGGAGGC 109 1748
    881935 N/A N/A 5903 5918 ACAGAGGTGGGAGTAC 174 1749
    881959 N/A N/A 6285 6300 TATAACCGGTAGAGTG 79 1750
    881981 N/A N/A 6697 6712 ACGATGATAGCTCACC 92 1751
    882005 N/A N/A 7221 7236 TACATTGAGGCATACA 59 1752
    882029 N/A N/A 7547 7562 CCCAAGTGAGGTCACC 80 1753
    882053 N/A N/A 7837 7852 GGCTCCTACATGTTTG 146 1754
    882077 N/A N/A 8222 8237 ACATGATAAGGCACTA 39 1755
    882100 N/A N/A 8470 8485 GCCGAAGCATTTTATC 71 1756
    882124 N/A N/A 8782 8797 GTTAAAGGAGTGCAGG 114 1757
    882147 N/A N/A 9461 9476 TCCCACGAAGGGCAGT 94 1758
    882170 N/A N/A 9788 9803 TCATTTTGATGTCTGG 37 1759
    882193 N/A N/A 10078 10093 GCCAATGCAACTGAAT 64 1760
    882217 N/A N/A 10202 10217 GTTACTAATTCCATAG 51 1761
    882241 N/A N/A 10525 10540 GACAGATGACATGCTT 91 1762
    882265 N/A N/A 10940 10955 GAGCAAACCCTGCACT 116 1763
    882289 N/A N/A 11216 11231 AGGTAAAGGCACATTC 81 1764
    882313 N/A N/A 11469 11484 TCAGATTGAATCCATA 36 1765
    882337 N/A N/A 11793 11808 AGCTGGTAGGTCAAAC 105 1766
    882361 N/A N/A 12050 12065 TTCGAGGTGATTCTCG 95 1767
    882385 N/A N/A 12284 12299 TGGTAACTGTATGGAA 52 1768
    882408 N/A N/A 12758 12773 AGAATTAGGTGCTTAA 39 1769
    882431 N/A N/A 13064 13079 CTATTATAGAGCATCA 45 1770
    882455 N/A N/A 13356 13371 GGCCAACGACTCCACA 77 1771
    882477 N/A N/A 14022 14037 TTAAGAGGCGACTGCT 88 1772
    882499 N/A N/A 14244 14259 CTTATAGCACTCTCCT 67 1773
    882522 N/A N/A 14645 14660 AGTACGAGCACATGTC 66 1774
    882545 N/A N/A 15191 15206 AAGGATGGGACCGCCC 61 1775
    882569 N/A N/A 15613 15628 AGATTAATAGTAAGTT 96 1776
    882592 N/A N/A 15864 15879 ACACAGGCTAATCAGA 93 1777
    882615 N/A N/A 16100 16115 ATCAGATACACACCCT 108 1778
    882639 N/A N/A 16278 16293 CAAAACGGACTGGAAC 84 1779
    882662 N/A N/A 16517 16532 CGTAACTCAGGCACCA 70 1780
    882686 N/A N/A 16762 16777 GACAGCTAAAGAACAC 81 1781
    882710 N/A N/A 16993 17008 CCACAAGAAAGAGACC 109 1782
    882734 N/A N/A 17400 17415 CGACAACTTTCCTGAA 79 1783
    882758 N/A N/A 17644 17659 CAAATATCATATGCCC 31 1784
    882782 N/A N/A 17904 17919 TAATAATGCTTGCAAG 88 1785
    882806 N/A N/A 18135 18150 AGTCAATCACTGGAGA 40 1786
    882829 N/A N/A 18691 18706 ATTCATTTTATGGACC 58 1787
    882853 N/A N/A 19108 19123 GGTAATTTAGGCCAAT 65 1788
    882876 N/A N/A 19366 19381 CTAAGGAGACAGTAAC 71 1789
  • TABLE 26
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID: SEQ ID: SEQ ID: IRF4 SEQ
    Compound 1 Start 1 Stop 2 Start 2 Stop (% ID
    Number Site Site Site Site Sequence UTC) NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 42 195
    881088 157 172 5184 5199 CGCTCATGCCGAACTC 89 1790
    881111 485 500 6964 6979 TACACTTTGTACGGGT 72 1791
    881135 782 797 10847 10862 GCACAAGCATAAAAGG 84 1792
    881158 1062 1077 13615 13630 GAGGACCACGCCCCTC 103 1793
    881182 1269 1284 17062 17077 GCATAGAGTCACCTGG 61 1794
    881206 1459 1474 19576 19591 GAATAGAGGAATGGCG 61 1795
    881230 1832 1847 19949 19964 TGCCAATCAGATGTCA 78 1796
    881254 1975 1990 20092 20107 GACCTAATCTACAACA 67 1797
    881278 2150 2165 20267 20282 AAGTGTCTTCCACAAG 46 1798
    881302 2310 2325 20427 20442 GTTTACTAACTGGCTT 73 1799
    881326 2443 2458 20560 20575 TAAAGAATGAGGGTCA 55 1800
    881350 2543 2558 20660 20675 GAACAGATAGTTAAGT 83 1801
    881374 2771 2786 20888 20903 TTTTAAGGCCCTGTCA 82 1802
    881398 2843 2858 20960 20975 TGATAGGTATACTTAA 72 1803
    881422 2957 2972 21074 21089 CGCAATCTTCTGCTGA 36 1804
    881446 3079 3094 21196 21211 GCTCACTAAGCTTGAT 44 1805
    881470 3390 3405 21507 21522 GGTAAATCTTCACTGT 35 1806
    881494 3475 3490 21592 21607 ATCCATGTTGCATGGC 39 1807
    881517 3561 3576 21678 21693 TAGGATAATATACCCC 26 1808
    881541 3734 3749 21851 21866 GCAATTGAAATGGAGC 76 1809
    881565 3979 3994 22096 22111 AGGAAGCCGTTCCTTT 58 1810
    881589 4201 4216 22318 22333 CTCTATAGTGTTCCAG 34 1811
    881608 4381 4396 22498 22513 ACTGTAAGGGCTGCTC 31 1812
    881632 4495 4510 22612 22627 GAGTACCCAAGACTCC 75 1813
    881656 4588 4603 22705 22720 GTTTACACTGGATCTG 39 1814
    881680 4765 4780 22882 22897 CAAAATGGTGTGTAAG 75 1815
    881704 4983 4998 23100 23115 GAATTTCCATTGGAGG 57 1816
    881728 5187 5202 23304 23319 CTCAGTTTGTGAAGCA 15 1817
    881752 5224 5239 23341 23356 TCATGATGTATACCAA 35 1818
    881776 N/A N/A 18810 18825 AATCATGATATTAGAG 69 1819
    881800 N/A N/A 3880 3895 CTGGAGGTCGAACCTC 98 1820
    881821 N/A N/A 4257 4272 GGTGAGCACCGCGCCG 108 1821
    881844 N/A N/A 4522 4537 GCCCAGCTAGCGCGCA 71 1822
    881868 N/A N/A 4909 4924 GCGCATCCCCTGGGCG 104 1823
    881892 N/A N/A 5538 5553 CCGCTGAGAGCCGAGG 104 1824
    881915 N/A N/A 5730 5745 GGGACCCACGGACGGA 91 1825
    881936 N/A N/A 5972 5987 CTCTAGACAGAGGCCC 80 1826
    881960 N/A N/A 6286 6301 TTATAACCGGTAGAGT 62 1827
    881982 N/A N/A 6761 6776 GGTTTATTAGCTTTCT 101 1828
    882006 N/A N/A 7226 7241 CCATATACATTGAGGC 56 1829
    882030 N/A N/A 7574 7589 ATAAAGGACCCCGCCA 82 1830
    882054 N/A N/A 8019 8034 GGCAAGTTCTGCTGTC 42 1831
    882078 N/A N/A 8226 8241 TTTCACATGATAAGGC 57 1832
    882101 N/A N/A 8471 8486 AGCCGAAGCATTTTAT 56 1833
    882125 N/A N/A 9093 9108 CTAAAGGAGTGCAGGA 94 1834
    882148 N/A N/A 9467 9482 ATAAGATCCCACGAAG 142 1835
    882171 N/A N/A 9816 9831 AGCTAATGAGAGCTTC 83 1836
    882194 N/A N/A 10086 10101 CTTGAAAAGCCAATGC 42 1837
    882218 N/A N/A 10203 10218 GGTTACTAATTCCATA 44 1838
    882242 N/A N/A 10526 10541 AGACAGATGACATGCT 50 1839
    882266 N/A N/A 11013 11028 TCTAAAGTCCCATCGA 69 1840
    882290 N/A N/A 11220 11235 GTAAAGGTAAAGGCAC 58 1841
    882314 N/A N/A 11528 11543 GGTAAGATCTCCATGG 55 1842
    882338 N/A N/A 11798 11813 GAAAGAGCTGGTAGGT 100 1843
    882362 N/A N/A 12054 12069 GCCATTCGAGGTGATT 44 1844
    882386 N/A N/A 12355 12370 ACCAAGCTGGGTTTGC 47 1845
    882409 N/A N/A 12760 12775 ATAGAATTAGGTGCTT 36 1846
    882432 N/A N/A 13065 13080 CCTATTATAGAGCATC 32 1847
    882456 N/A N/A 13361 13376 CTCGAGGCCAACGACT 99 1848
    882478 N/A N/A 14025 14040 GTTTTAAGAGGCGACT 67 1849
    882500 N/A N/A 14246 14261 AACTTATAGCACTCTC 72 1850
    882523 N/A N/A 14648 14663 AGAAGTACGAGCACAT 56 1851
    882546 N/A N/A 15192 15207 GAAGGATGGGACCGCC 59 1852
    882570 N/A N/A 15617 15632 TCACAGATTAATAGTA 77 1853
    882593 N/A N/A 15867 15882 CCTACACAGGCTAATC 87 1854
    882616 N/A N/A 16101 16116 TATCAGATACACACCC 81 1855
    882640 N/A N/A 16279 16294 ACAAAACGGACTGGAA 86 1856
    882663 N/A N/A 16535 16550 TGCTACTGCGGACATC 57 1857
    882687 N/A N/A 16763 16778 CGACAGCTAAAGAACA 63 1858
    882711 N/A N/A 17000 17015 TAGAAGCCCACAAGAA 99 1859
    882735 N/A N/A 17402 17417 TACGACAACTTTCCTG 59 1860
    882759 N/A N/A 17662 17677 GAAAGATTCAGCCTCT 55 1861
    882783 N/A N/A 17906 17921 GTTAATAATGCTTGCA 98 1862
    882807 N/A N/A 18141 18156 TTATTAAGTCAATCAC 101 1863
    882830 N/A N/A 18714 18729 CTCATAGGTGTACACG 41 1864
    882854 N/A N/A 19114 19129 CTGCAGGGTAATTTAG 66 1865
    882877 N/A N/A 19379 19394 CAGCACTCAGATTCTA 88 1866
  • TABLE 27
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID: SEQ ID: SEQ ID: IRF4 SEQ
    Compound 1 Start 1 Stop 2 Start 2 Stop (% ID
    Number Site Site Site Site Sequence UTC) NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 41 195
    668855 783 798 10848 10863 GGCACAAGCATAAAAG 99 1867
    690520 4222 4237 22339 22354 AAATGAGTCGGTCACT 45 1868
    881089 165 180 5192 5207 GCTCACCGCGCTCATG 52 1869
    881112 486 501 6965 6980 GTACACTTTGTACGGG 36 1870
    881159 1067 1082 13620 13635 ATCCAGAGGACCACGC 81 1871
    881183 1270 1285 17063 17078 AGCATAGAGTCACCTG 37 1872
    881207 1460 1475 19577 19592 TGAATAGAGGAATGGC 79 1873
    881231 1844 1859 19961 19976 AATAAGCTCATCTGCC 64 1874
    881255 1978 1993 20095 20110 CAAGACCTAATCTACA 88 1875
    881279 2151 2166 20268 20283 CAAGTGTCTTCCACAA 35 1876
    881303 2311 2326 20428 20443 AGTTTACTAACTGGCT 37 1877
    881327 2444 2459 20561 20576 CTAAAGAATGAGGGTC 38 1878
    881351 2545 2560 20662 20677 GGGAACAGATAGTTAA 74 1879
    881375 2773 2788 20890 20905 AATTTTAAGGCCCTGT 76 1880
    881399 2844 2859 20961 20976 GTGATAGGTATACTTA 35 1881
    881423 2958 2973 21075 21090 ACGCAATCTTCTGCTG 48 1882
    881447 3086 3101 21203 21218 GCTCACTGCTCACTAA 67 1883
    881471 3391 3406 21508 21523 AGGTAAATCTTCACTG 46 1884
    881495 3479 3494 21596 21611 ACATATCCATGTTGCA 21 1885
    881518 3562 3577 21679 21694 TTAGGATAATATACCC 48 1886
    881542 3785 3800 21902 21917 ACTGTTAAAGCAGCAT 29 1887
    881566 3980 3995 22097 22112 GAGGAAGCCGTTCCTT 49 1888
    881609 4383 4398 22500 22515 ATACTGTAAGGGCTGC 46 1889
    881633 4504 4519 22621 22636 AAGAGGTGCGAGTACC 66 1890
    881657 4590 4605 22707 22722 AAGTTTACACTGGATC 42 1891
    881681 4786 4801 22903 22918 GGGCATGTAAAACATA 77 1892
    881705 4985 5000 23102 23117 GGGAATTTCCATTGGA 56 1893
    881729 5188 5203 23305 23320 CCTCAGTTTGTGAAGC 31 1894
    881753 5226 5241 23343 23358 ATTCATGATGTATACC 38 1895
    881777 N/A N/A 18811 18826 CAATCATGATATTAGA 62 1896
    881801 N/A N/A 3897 3912 GGGTACCCTGCGCTGC 56 1897
    881822 N/A N/A 4292 4307 CCAAATGTGGAGCTCC 77 1898
    881845 N/A N/A 4542 4557 CGAATAGGACCCCTAT 91 1899
    881869 N/A N/A 4916 4931 GGCCCGGGCGCATCCC 95 1900
    881893 N/A N/A 5548 5563 CCCCGCGGTCCCGCTG 59 1901
    881916 N/A N/A 5749 5764 ACGCACGGAGAGGGCG 99 1902
    881937 N/A N/A 5974 5989 AGCTCTAGACAGAGGC 65 1903
    881961 N/A N/A 6287 6302 TTTATAACCGGTAGAG 46 1904
    881983 N/A N/A 6783 6798 CGAAAAGTCAAAATAC 100 1905
    882007 N/A N/A 7228 7243 CCCCATATACATTGAG 63 1906
    882031 N/A N/A 7576 7591 ACATAAAGGACCCCGC 72 1907
    882055 N/A N/A 8027 8042 TAGCAAATGGCAAGTT 83 1908
    882079 N/A N/A 8248 8263 GAAGAGATCAGCTGCC 58 1909
    882102 N/A N/A 8475 8490 TGACAGCCGAAGCATT 62 1910
    882126 N/A N/A 9094 9109 GCTAAAGGAGTGCAGG 93 1911
    882149 N/A N/A 9468 9483 AATAAGATCCCACGAA 85 1912
    882172 N/A N/A 9820 9835 ACCCAGCTAATGAGAG 65 1913
    882195 N/A N/A 10098 10113 CTGCAAATCCCTCTTG 133 1914
    882219 N/A N/A 10230 10245 CAGTTCTAAGCATTGC 67 1915
    882243 N/A N/A 10551 10566 GACTAACAGGGAGACT 109 1916
    882267 N/A N/A 11014 11029 GTCTAAAGTCCCATCG 60 1917
    882291 N/A N/A 11251 11266 CGTGAGAATGTTGGCT 51 1918
    882315 N/A N/A 11533 11548 TAGTAGGTAAGATCTC 77 1919
    882339 N/A N/A 11799 11814 AGAAAGAGCTGGTAGG 64 1920
    882363 N/A N/A 12074 12089 CCCAAAGAGAGTGGGT 100 1921
    882387 N/A N/A 12364 12379 GTTGAAAGAACCAAGC 89 1922
    882410 N/A N/A 12761 12776 TATAGAATTAGGTGCT 60 1923
    882433 N/A N/A 13112 13127 GGAACAAGTGTATCTT 24 1924
    882457 N/A N/A 13367 13382 CACCACCTCGAGGCCA 76 1925
    882479 N/A N/A 14027 14042 CTGTTTTAAGAGGCGA 42 1926
    882501 N/A N/A 14250 14265 AGCCAACTTATAGCAC 46 1927
    882524 N/A N/A 14649 14664 CAGAAGTACGAGCACA 53 1928
    882547 N/A N/A 15195 15210 CAAGAAGGATGGGACC 75 1929
    882571 N/A N/A 15619 15634 GCTCACAGATTAATAG 84 1930
    882594 N/A N/A 15871 15886 TACACCTACACAGGCT 81 1931
    882617 N/A N/A 16121 16136 CTGCAGAACAGACGCG 89 1932
    882641 N/A N/A 16280 16295 TACAAAACGGACTGGA 62 1933
    882664 N/A N/A 16551 16566 CATAATCCAGTATCTG 82 1934
    882688 N/A N/A 16767 16782 TAGTCGACAGCTAAAG 54 1935
    882712 N/A N/A 17001 17016 GTAGAAGCCCACAAGA 104 1936
    882736 N/A N/A 17404 17419 AATACGACAACTTTCC 50 1937
    882760 N/A N/A 17664 17679 TTGAAAGATTCAGCCT 97 1938
    882784 N/A N/A 17918 17933 GCATGCAAGCCCGTTA 101 1939
    882808 N/A N/A 18183 18198 TTGTTAACAATGTATC 53 1940
    882831 N/A N/A 18715 18730 ACTCATAGGTGTACAC 55 1941
    882855 N/A N/A 19126 19141 GTCTGAGGGAATCTGC 51 1942
    882878 N/A N/A 19384 19399 TTAAACAGCACTCAGA 67 1943
  • TABLE 28
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID: SEQ ID: SEQ ID: IRF4 SEQ
    Compound 1 Start 1 Stop 2 Start 2 Stop (% ID
    Number Site Site Site Site Sequence UTC) NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 20 195
    690521 4224 4239 22341 22356 GTAAATGAGTCGGTCA 21 1944
    881090 170 185 5197 5212 CCGCAGCTCACCGCGC 64 1945
    881113 488 503 6967 6982 CTGTACACTTTGTACG 66 1946
    881136 837 852 10902 10917 GGCAGACCTTATGCTT 79 1947
    881160 1071 1086 13624 13639 GGCCATCCAGAGGACC 75 1948
    881184 1271 1286 17064 17079 AAGCATAGAGTCACCT 64 1949
    881208 1461 1476 19578 19593 TTGAATAGAGGAATGG 58 1950
    881232 1886 1901 20003 20018 GTCTACAGAACACAAG 76 1951
    881256 1984 1999 20101 20116 TTCCAGCAAGACCTAA 73 1952
    881280 2152 2167 20269 20284 GCAAGTGTCTTCCACA 23 1953
    881304 2312 2327 20429 20444 AAGTTTACTAACTGGC 37 1954
    881328 2462 2477 20579 20594 CGAAGAATTTTAGCAT 42 1955
    881352 2546 2561 20663 20678 AGGGAACAGATAGTTA 66 1956
    881376 2774 2789 20891 20906 TAATTTTAAGGCCCTG 61 1957
    881400 2845 2860 20962 20977 AGTGATAGGTATACTT 61 1958
    881424 2962 2977 21079 21094 AGCTACGCAATCTTCT 53 1959
    881448 3250 3265 21367 21382 ACTTTTAGAGAGGAGA 36 1960
    881472 3394 3409 21511 21526 ACGAGGTAAATCTTCA 39 1961
    881496 3480 3495 21597 21612 TACATATCCATGTTGC 26 1962
    881519 3564 3579 21681 21696 CCTTAGGATAATATAC 77 1963
    881543 3787 3802 21904 21919 CCACTGTTAAAGCAGC 34 1964
    881567 3983 3998 22100 22115 AATGAGGAAGCCGTTC 53 1965
    881610 4384 4399 22501 22516 AATACTGTAAGGGCTG 36 1966
    881634 4506 4521 22623 22638 CCAAGAGGTGCGAGTA 67 1967
    881658 4591 4606 22708 22723 GAAGTTTACACTGGAT 35 1968
    881682 4802 4817 22919 22934 ATCAGTCTCAAAAACG 59 1969
    881706 4989 5004 23106 23121 ACACGGGAATTTCCAT 44 1970
    881730 5189 5204 23306 23321 ACCTCAGTTTGTGAAG 61 1971
    881754 5248 5263 23365 23380 TTGCAGAGCAATTTAC 50 1972
    881778 N/A N/A 18814 18829 CATCAATCATGATATT 75 1973
    881823 N/A N/A 4304 4319 GCTCGGAGCGACCCAA 92 1974
    881846 N/A N/A 4543 4558 CCGAATAGGACCCCTA 68 1975
    881870 N/A N/A 4920 4935 GGCCGGCCCGGGCGCA 99 1976
    881894 N/A N/A 5566 5581 CAGGACCCGGCTCCCG 86 1977
    881917 N/A N/A 5752 5767 CGGACGCACGGAGAGG 72 1978
    881938 N/A N/A 5982 5997 AGGGAGACAGCTCTAG 75 1979
    881962 N/A N/A 6290 6305 GTATTTATAACCGGTA 33 1980
    881984 N/A N/A 7014 7029 CAAATTCAGGAGAGCC 81 1981
    882008 N/A N/A 7247 7262 ACATATTCAATGCACC 53 1982
    882032 N/A N/A 7578 7593 TGACATAAAGGACCCC 52 1983
    882056 N/A N/A 8032 8047 AGCCATAGCAAATGGC 95 1984
    882080 N/A N/A 8302 8317 CTTTTACCCACCAAAG 82 1985
    882103 N/A N/A 8481 8496 TTAGACTGACAGCCGA 47 1986
    882127 N/A N/A 9278 9293 CAATTAGCTCTTCTAT 86 1987
    882150 N/A N/A 9471 9486 TTAAATAAGATCCCAC 77 1988
    882173 N/A N/A 9835 9850 CTAGATTCTCCCTGCA 66 1989
    882196 N/A N/A 10110 10125 AACCAGCCCTTGCTGC 79 1990
    882220 N/A N/A 10237 10252 CTTTACACAGTTCTAA 113 1991
    882244 N/A N/A 10554 10569 ACTGACTAACAGGGAG 51 1992
    882268 N/A N/A 11021 11036 AGCAAGTGTCTAAAGT 38 1993
    882292 N/A N/A 11271 11286 TCCAAGCAATTATTCC 88 1994
    882316 N/A N/A 11534 11549 ATAGTAGGTAAGATCT 113 1995
    882340 N/A N/A 11800 11815 TAGAAAGAGCTGGTAG 91 1996
    882364 N/A N/A 12075 12090 CCCCAAAGAGAGTGGG 111 1997
    882388 N/A N/A 12372 12387 GCCCATGAGTTGAAAG 68 1998
    882411 N/A N/A 12762 12777 ATATAGAATTAGGTGC 84 1999
    882434 N/A N/A 13113 13128 AGGAACAAGTGTATCT 54 2000
    882502 N/A N/A 14254 14269 ACAGAGCCAACTTATA 94 2001
    882525 N/A N/A 14652 14667 ACCCAGAAGTACGAGC 79 2002
    882548 N/A N/A 15218 15233 CCCATGAACACCATGC 68 2003
    882572 N/A N/A 15635 15650 GCCAAGACCAGCTCTT 70 2004
    882595 N/A N/A 15872 15887 CTACACCTACACAGGC 84 2005
    882618 N/A N/A 16132 16147 CGCTACAGCTTCTGCA 80 2006
    882642 N/A N/A 16281 16296 ATACAAAACGGACTGG 85 2007
    882665 N/A N/A 16553 16568 CACATAATCCAGTATC 57 2008
    882689 N/A N/A 16773 16788 AGGAACTAGTCGACAG 60 2009
    882713 N/A N/A 17133 17148 TGTAACTGAGGACTCA 102 2010
    882737 N/A N/A 17405 17420 AAATACGACAACTTTC 79 2011
    882761 N/A N/A 17676 17691 TGCTTGAATTCCTTGA 33 2012
    882785 N/A N/A 17923 17938 GCTCAGCATGCAAGCC 100 2013
    882809 N/A N/A 18225 18240 GCTTATCAATGCCAAG 60 2014
    882832 N/A N/A 18716 18731 AACTCATAGGTGTACA 39 2015
    882856 N/A N/A 19154 19169 TCAAGTAAAGTGATCA 52 2016
    882879 N/A N/A 19387 19402 CTATTAAACAGCACTC 82 2017
    882890 N/A N/A 3949 3964 GTGGGAGTCGGAGCTC 83 2018
    882906 N/A N/A 13375 13390 GCCAAGGACACCACCT 102 2019
    882908 N/A N/A 14061 14076 GTATTTGTCGAGATCA 41 2020
  • TABLE 29
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID:  SEQ ID: SEQ ID: IRF4 SEQ
    Compound 1 Start 1 Stop 2 Start 2 Stop (% ID 
    Number Site Site Site Site Sequence UTC) NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT  33  195
    690522 4228 4243 22345 22360 AGTTGTAAATGAGTCG  15 2021
    881091  186  201  5213 5228 GCGGAGCTTCCCGTTG  67 2022
    881114  495  510  6974 6989 AACAATCCTGTACACT  78 2023
    881161 1088 1103 13641 13656 GCATAGAGCCCGTCGG  50 2024
    881185 1272 1287 17065 17080 AAAGCATAGAGTCACC  66 2025
    881209 1532 1547 19649 19664 CCGTATCCCCGTATCA  65 2026
    881233 1891 1906 20008 20023 TGGCAGTCTACAGAAC 122 2027
    881257 2001 2016 20118 20133 GGCAAGTTTTCTCTGT  64 2028
    881281 2154 2169 20271 20286 CAGCAAGTGTCTTCCA  36 2029
    881305 2313 2328 20430 20445 GAAGTTTACTAACTGG  43 2030
    881329 2463 2478 20580 20595 GCGAAGAATTTTAGCA  88 2031
    881353 2547 2562 20664 20679 AAGGGAACAGATAGTT  80 2032
    881377 2775 2790 20892 20907 GTAATTTTAAGGCCCT  45 2033
    881401 2846 2861 20963 20978 AAGTGATAGGTATACT  50 2034
    881425 2965 2980 21082 21097 GAGAGCTACGCAATCT  43 2035
    881449 3251 3266 21368 21383 CACTTTTAGAGAGGAG  38 2036
    881473 3395 3410 21512 21527 AACGAGGTAAATCTTC  49 2037
    881497 3484 3499 21601 21616 CCAATACATATCCATG  40 2038
    881520 3566 3581 21683 21698 TCCCTTAGGATAATAT  52 2039
    881544 3788 3803 21905 21920 TCCACTGTTAAAGCAG  45 2040
    881568 3984 3999 22101 22116 GAATGAGGAAGCCGTT  61 2041
    881611 4385 4400 22502 22517 CAATACTGTAAGGGCT  44 2042
    881635 4507 4522 22624 22639 GCCAAGAGGTGCGAGT  65 2043
    881659 4592 4607 22709 22724 GGAAGTTTACACTGGA  15 2044
    881683 4808 4823 22925 22940 ATCGAGATCAGTCTCA  24 2045
    881707 4991 5006 23108 23123 CAACACGGGAATTTCC  45 2046
    881731 5191 5206 23308 23323 CTACCTCAGTTTGTGA  59 2047
    881755 N/A N/A 18767 18782 CTAAACTCCTAAGTAC  86 2048
    881779 N/A N/A 18827 18842 GCTGAATGCTCTCCAT  48 2049
    881802 N/A N/A  3965  3980 GCTCAGCGCAGATGGG 102 2050
    881824 N/A N/A  4310  4325 CGCAAGGCTCGGAGCG  90 2051
    881847 N/A N/A  4544  4559 CCCGAATAGGACCCCT  60 2052
    881871 N/A N/A  4932  4947 AGGCACCTTCGCGGCC  82 2053
    881918 N/A N/A  5754  5769 CGCGGACGCACGGAGA  81 2054
    881939 N/A N/A  5995  6010 CGCGCAAAGGGCAAGG  66 2055
    881963 N/A N/A  6292  6307 GGGTATTTATAACCGG  41 2056
    881985 N/A N/A  7032  7047 TGCCTCTGTTAGGTGA  66 2057
    882009 N/A N/A  7268  7283 TTGAAAGACTAACTGG  80 2058
    882033 N/A N/A  7580  7595 TGTGACATAAAGGACC  73 2059
    882057 N/A N/A  8040  8055 GTTGGAGCAGCCATAG  69 2060
    882081 N/A N/A  8329  8344 CAAAAGTACCACAGGG  60 2061
    882104 N/A N/A  8484  8499 TTATTAGACTGACAGC  63 2062
    882128 N/A N/A  9279  9294 GCAATTAGCTCTTCTA  79 2063
    882151 N/A N/A  9525  9540 CTATATAAAAAGTGGG  84 2064
    882174 N/A N/A  9837  9852 TGCTAGATTCTCCCTG  67 2065
    882197 N/A N/A 10114 10129 TGGAAACCAGCCCTTG  52 2066
    882221 N/A N/A 10250 10265 ACCTACTCCATCACTT 103 2067
    882245 N/A N/A 10559 10574 CTGTAACTGACTAACA  77 2068
    882269 N/A N/A 11022 11037 AAGCAAGTGTCTAAAG  71 2069
    882293 N/A N/A 11278 11293 CTACACTTCCAAGCAA 105 2070
    882317 N/A N/A 11535 11550 TATAGTAGGTAAGATC  87 2071
    882341 N/A N/A 11801 11816 CTAGAAAGAGCTGGTA  85 2072
    882365 N/A N/A 12087 12102 TCAGACAGTGCGCCCC  74 2073
    882389 N/A N/A 12379 12394 AAATATCGCCCATGAG  61 2074
    882412 N/A N/A 12763 12778 TATATAGAATTAGGTG 116 2075
    882435 N/A N/A 13115 13130 TAAGGAACAAGTGTAT  82 2076
    882458 N/A N/A 13393 13408 CCGGAGTCAGTGCTGG 107 2077
    882480 N/A N/A 14062 14077 CGTATTTGTCGAGATC  50 2078
    882503 N/A N/A 14256 14271 TCACAGAGCCAACTTA 112 2079
    882526 N/A N/A 14656 14671 TTACACCCAGAAGTAC  95 2080
    882549 N/A N/A 15312 15327 GCCCATGTGAGCTCTT  50 2081
    882573 N/A N/A 15704 15719 GAACACTTTGAGGTGA  86 2082
    882596 N/A N/A 15874 15889 GACTACACCTACACAG  68 2083
    882619 N/A N/A 16135 16150 AGCCGCTACAGCTTCT 108 2084
    882643 N/A N/A 16282 16297 GATACAAAACGGACTG  56 2085
    882666 N/A N/A 16556 16571 GCCCACATAATCCAGT  78 2086
    882690 N/A N/A 16774 16789 GAGGAACTAGTCGACA  61 2087
    882714 N/A N/A 17139 17154 TAGGAGTGTAACTGAG  63 2088
    882738 N/A N/A 17406 17421 GAAATACGACAACTTT  78 2089
    882762 N/A N/A 17693 17708 TACGAGAGGGTCTGAT 100 2090
    882786 N/A N/A 17936 17951 TTTACCTGGTATTGCT  62 2091
    882810 N/A N/A 18226 18241 TGCTTATCAATGCCAA  30 2092
    882833 N/A N/A 18717 18732 GAACTCATAGGTGTAC  33 2093
    882880 N/A N/A 19389 19404 CACTATTAAACAGCAC  81 2094
    882916 N/A N/A 19155 19170 ATCAAGTAAAGTGATC  71 2095
  • TABLE 30
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID: SEQ ID: SEQ ID: IRF4  SEQ
    Compound 1 Start 1 Stop 2 Start 2 Stop (% ID 
    Number Site Site Site Site Sequence UTC) NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 29 195
    690523 4230 4245 22347 22362 TCAGTTGTAAATGAGT 28 2096
    881092 187 202 5214 5229 GGCGGAGCTTCCCGTT 74 2097
    881115 498 513 6977 6992 AGGAACAATCCTGTAC 84 2098
    881162 1089 1104 13642 13657 CGCATAGAGCCCGTCG 47 2099
    881186 1273 1288 17066 17081 CAAAGCATAGAGTCAC 64 2100
    881210 1534 1549 19651 19666 CCCCGTATCCCCGTAT 55 2101
    881234 1896 1911 20013 20028 AATGATGGCAGTCTAC 67 2102
    881258 2014 2029 20131 20146 GTCAATACTGAAAGGC 34 2103
    881282 2155 2170 20272 20287 TCAGCAAGTGTCTTCC 34 2104
    881306 2316 2331 20433 20448 TAGGAAGTTTACTAAC 64 2105
    881330 2464 2479 20581 20596 TGCGAAGAATTTTAGC 59 2106
    881354 2548 2563 20665 20680 GAAGGGAACAGATAGT 83 2107
    881378 2776 2791 20893 20908 AGTAATTTTAAGGCCC 40 2108
    881402 2847 2862 20964 20979 TAAGTGATAGGTATAC 40 2109
    881426 2972 2987 21089 21104 CACATTTGAGAGCTAC 26 2110
    881450 3252 3267 21369 21384 ACACTTTTAGAGAGGA 37 2111
    881474 3396 3411 21513 21528 GAACGAGGTAAATCTT 44 2112
    881498 3485 3500 21602 21617 CCCAATACATATCCAT 26 2113
    881521 3600 3615 21717 21732 CGTGAAACAGCAGTTC 60 2114
    881545 3789 3804 21906 21921 CTCCACTGTTAAAGCA 48 2115
    881569 3986 4001 22103 22118 AGGAATGAGGAAGCCG 44 2116
    881612 4387 4402 22504 22519 AACAATACTGTAAGGG 49 2117
    881636 4508 4523 22625 22640 AGCCAAGAGGTGCGAG 62 2118
    881660 4593 4608 22710 22725 CGGAAGTTTACACTGG 15 2119
    881684 4809 4824 22926 22941 CATCGAGATCAGTCTC 35 2120
    881708 4993 5008 23110 23125 AGCAACACGGGAATTT 43 2121
    881732 5197 5212 23314 23329 CATTATCTACCTCAGT 65 2122
    881756 N/A N/A 18768 18783 GCTAAACTCCTAAGTA 70 2123
    881780 N/A N/A 18828 18843 AGCTGAATGCTCTCCA 22 2124
    881803 N/A N/A 3993 4008 GGCCTTGGAGCCCAAA 80 2125
    881825 N/A N/A 4311 4326 ACGCAAGGCTCGGAGC 79 2126
    881848 N/A N/A 4545 4560 CCCCGAATAGGACCCC 44 2127
    881872 N/A N/A 4937 4952 GAAGAAGGCACCTTCG 75 2128
    881896 N/A N/A 5646 5661 GCAAAACCCCTCAAGC 80 2129
    881919 N/A N/A 5755 5770 GCGCGGACGCACGGAG 98 2130
    881940 N/A N/A 6001 6016 TGCACTCGCGCAAAGG 72 2131
    881964 N/A N/A 6315 6330 GCCAAGTTGAAGACAC 43 2132
    881986 N/A N/A 7057 7072 AGTTAAGGTGCCTCAA 101 2133
    882010 N/A N/A 7304 7319 TAACAAGTTATCCAGT 88 2134
    882034 N/A N/A 7593 7608 TGCGAATGTGCCTTGT 57 2135
    882058 N/A N/A 8095 8110 CAGCACCGTGTGGAAA 49 2136
    882082 N/A N/A 8335 8350 TGGCACCAAAAGTACC 66 2137
    882105 N/A N/A 8485 8500 CTTATTAGACTGACAG 59 2138
    882129 N/A N/A 9287 9302 CCACATTAGCAATTAG 81 2139
    882152 N/A N/A 9550 9565 TTTATGAGCTTCCACA 46 2140
    882175 N/A N/A 9843 9858 CCGCATTGCTAGATTC 28 2141
    882198 N/A N/A 10115 10130 TTGGAAACCAGCCCTT 61 2142
    882222 N/A N/A 10253 10268 TCTACCTACTCCATCA 53 2143
    882246 N/A N/A 10580 10595 AGGAAACTTGGAGCGC 23 2144
    882270 N/A N/A 11025 11040 GCAAAGCAAGTGTCTA 57 2145
    882294 N/A N/A 11313 11328 GAAGGATGATCAGCTT 74 2146
    882318 N/A N/A 11536 11551 TTATAGTAGGTAAGAT 98 2147
    882342 N/A N/A 11819 11834 TGCAAGCCTCATTCAC 58 2148
    882366 N/A N/A 12089 12104 AGTCAGACAGTGCGCC 90 2149
    882390 N/A N/A 12380 12395 AAAATATCGCCCATGA 59 2150
    882413 N/A N/A 12827 12842 TGACATCATTTAGGTA 46 2151
    882436 N/A N/A 13133 13148 GGCCACCGACTCTTTT 87 2152
    882459 N/A N/A 13780 13795 ATAACGAGGTGCCTTA 87 2153
    882481 N/A N/A 14077 14092 CGCCACATCAGCAGAC 88 2154
    882527 N/A N/A 14658 14673 ACTTACACCCAGAAGT 110 2155
    882550 N/A N/A 15328 15343 GGCCTTAGCCTTCCTG 83 2156
    882574 N/A N/A 15765 15780 GCAGAAGCTGGTTGGC 42 2157
    882597 N/A N/A 15877 15892 TGAGACTACACCTACA 81 2158
    882620 N/A N/A 16140 16155 ACAGGAGCCGCTACAG 69 2159
    882644 N/A N/A 16284 16299 AAGATACAAAACGGAC 61 2160
    882667 N/A N/A 16568 16583 CCTCACTACAGAGCCC 76 2161
    882691 N/A N/A 16778 16793 TCAAGAGGAACTAGTC 76 2162
    882715 N/A N/A 17140 17155 GTAGGAGTGTAACTGA 59 2163
    882739 N/A N/A 17407 17422 GGAAATACGACAACTT 37 2164
    882763 N/A N/A 17694 17709 TTACGAGAGGGTCTGA 49 2165
    882787 N/A N/A 17937 17952 TTTTACCTGGTATTGC 102 2166
    882811 N/A N/A 18247 18262 GATCATCAACTTCTTA 53 2167
    882834 N/A N/A 18719 18734 TGGAACTCATAGGTGT 38 2168
    882857 N/A N/A 19164 19179 CTGCATCAAATCAAGT 53 2169
    882881 N/A N/A 19390 19405 TCACTATTAAACAGCA 84 2170
    882910 N/A N/A 14263 14278 GTTCATATCACAGAGC 55 2171
  • TABLE 31
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID: SEQ ID: SEQ ID: IRF4 SEQ
    Compound 1 Start 1 Stop 2 Start 2 Stop (% ID
    Number Site Site Site Site Sequence UTC) NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 23 195
    690526 4234 4249 22351 22366 GGTTTCAGTTGTAAAT 42 2172
    881093 193 208 5220 5235 GCCACTGGCGGAGCTT 77 2173
    881116 554 569 7872 7887 ATGGACATCTGCGGGT 50 2174
    881163 1090 1105 13643 13658 TCGCATAGAGCCCGTC 43 2175
    881187 1274 1289 17067 17082 CCAAAGCATAGAGTCA 42 2176
    881211 1539 1554 19656 19671 CAAGACCCCGTATCCC 56 2177
    881235 1897 1912 20014 20029 CAATGATGGCAGTCTA 60 2178
    881259 2015 2030 20132 20147 TGTCAATACTGAAAGG 64 2179
    881283 2156 2171 20273 20288 CTCAGCAAGTGTCTTC 55 2180
    881307 2317 2332 20434 20449 ATAGGAAGTTTACTAA 87 2181
    881331 2465 2480 20582 20597 ATGCGAAGAATTTTAG 79 2182
    881355 2583 2598 20700 20715 GGACAGCCAAACAAAC 93 2183
    881379 2778 2793 20895 20910 CAAGTAATTTTAAGGC 59 2184
    881403 2849 2864 20966 20981 TGTAAGTGATAGGTAT 47 2185
    881427 2973 2988 21090 21105 ACACATTTGAGAGCTA 31 2186
    881451 3254 3269 21371 21386 GGACACTTTTAGAGAG 38 2187
    881475 3397 3412 21514 21529 AGAACGAGGTAAATCT 60 2188
    881499 3486 3501 21603 21618 GCCCAATACATATCCA 42 2189
    881522 3601 3616 21718 21733 CCGTGAAACAGCAGTT 44 2190
    881546 3791 3806 21908 21923 AGCTCCACTGTTAAAG 56 2191
    881570 3999 4014 22116 22131 CTTTATCAAGACAAGG 44 2192
    881613 4388 4403 22505 22520 TAACAATACTGTAAGG 55 2193
    881637 4523 4538 22640 22655 GCGGAGCATCAACAAA 70 2194
    881661 4594 4609 22711 22726 ACGGAAGTTTACACTG 23 2195
    881685 4810 4825 22927 22942 GCATCGAGATCAGTCT 43 2196
    881709 4994 5009 23111 23126 AAGCAACACGGGAATT 78 2197
    881733 5198 5213 23315 23330 GCATTATCTACCTCAG 31 2198
    881757 N/A N/A 18769 18784 AGCTAAACTCCTAAGT 85 2199
    881781 N/A N/A 18832 18847 GGCAAGCTGAATGCTC 71 2200
    881804 N/A N/A 4002 4017 AAGGAGGCGGGCCTTG 98 2201
    881826 N/A N/A 4315 4330 CCGCACGCAAGGCTCG 84 2202
    881849 N/A N/A 4563 4578 TCGCATCCAGACCCTT 72 2203
    881873 N/A N/A 4939 4954 CGGAAGAAGGCACCTT 112 2204
    881897 N/A N/A 5647 5662 CGCAAAACCCCTCAAG 81 2205
    881920 N/A N/A 5760 5775 CACAGGCGCGGACGCA 86 2206
    881941 N/A N/A 6021 6036 GTAACAACGACACACG 41 2207
    881965 N/A N/A 6325 6340 CCCTATCACTGCCAAG 62 2208
    881987 N/A N/A 7065 7080 CAGAATGAAGTTAAGG 50 2209
    882011 N/A N/A 7325 7340 GACTATTAGATAAGTA 71 2210
    882035 N/A N/A 7602 7617 CAGATGGCATGCGAAT 65 2211
    882059 N/A N/A 8097 8112 GGCAGCACCGTGTGGA 47 2212
    882083 N/A N/A 8344 8359 GGCTAAACCTGGCACC 60 2213
    882106 N/A N/A 8486 8501 CCTTATTAGACTGACA 52 2214
    882130 N/A N/A 9288 9303 GCCACATTAGCAATTA 92 2215
    882153 N/A N/A 9557 9572 CTTATTATTTATGAGC 63 2216
    882176 N/A N/A 9845 9860 TACCGCATTGCTAGAT 77 2217
    882199 N/A N/A 10119 10134 CATATTGGAAACCAGC 27 2218
    882223 N/A N/A 10264 10279 CAAGACAGGTCTCTAC 66 2219
    882247 N/A N/A 10581 10596 AAGGAAACTTGGAGCG 41 2220
    882271 N/A N/A 11026 11041 AGCAAAGCAAGTGTCT 42 2221
    882295 N/A N/A 11321 11336 TCAACCTGGAAGGATG 70 2222
    882319 N/A N/A 11537 11552 TTTATAGTAGGTAAGA 94 2223
    882343 N/A N/A 11827 11842 AAAAAAGGTGCAAGCC 93 2224
    882367 N/A N/A 12093 12108 AGCGAGTCAGACAGTG 84 2225
    882391 N/A N/A 12382 12397 TTAAAATATCGCCCAT 68 2226
    882414 N/A N/A 12871 12886 AGCAAGTCGGTCCACA 46 2227
    882437 N/A N/A 13154 13169 CAGCATATTACAAACG 42 2228
    882460 N/A N/A 13781 13796 GATAACGAGGTGCCTT 82 2229
    882504 N/A N/A 14295 14310 ACTCACTGGTTCTGAA 86 2230
    882528 N/A N/A 14661 14676 GTCACTTACACCCAGA 48 2231
    882551 N/A N/A 15359 15374 GTCCAGAGTCTTCAGA 94 2232
    882575 N/A N/A 15772 15787 TAATTATGCAGAAGCT 103 2233
    882598 N/A N/A 15879 15894 TCTGAGACTACACCTA 73 2234
    882621 N/A N/A 16146 16161 GTTGACACAGGAGCCG 47 2235
    882645 N/A N/A 16285 16300 AAAGATACAAAACGGA 62 2236
    882668 N/A N/A 16581 16596 TAAAACCTCATCCCCT 126 2237
    882692 N/A N/A 16779 16794 TTCAAGAGGAACTAGT 94 2238
    882716 N/A N/A 17146 17161 ACTATGGTAGGAGTGT 75 2239
    882740 N/A N/A 17409 17424 ATGGAAATACGACAAC 65 2240
    882764 N/A N/A 17696 17711 CATTACGAGAGGGTCT 56 2241
    882788 N/A N/A 17940 17955 AACTTTTACCTGGTAT 72 2242
    882812 N/A N/A 18251 18266 GGCCGATCATCAACTT 93 2243
    882835 N/A N/A 18720 18735 GTGGAACTCATAGGTG 47 2244
    882858 N/A N/A 19173 19188 TAACTAAAACTGCATC 90 2245
    882882 N/A N/A 19391 19406 CTCACTATTAAACAGC 76 2246
    882909 N/A N/A 14080 14095 AGCCGCCACATCAGCA 79 2247
  • TABLE 32
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID: SEQ ID: SEQ ID: IRF4 SEQ
    Compound 1 Start 1 Stop 2 Start 2 Stop (% ID
    Number Site Site Site Site Sequence UTC) NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 26 195
    881094 194 209 5221 5236 AGCCACTGGCGGAGCT 62 2248
    881117 558 573 7876 7891 GCTCATGGACATCTGC 61 2249
    881164 1097 1112 13650 13665 AGTCTTTTCGCATAGA 55 2250
    881188 1276 1291 17069 17084 CTCCAAAGCATAGAGT 77 2251
    881212 1685 1700 19802 19817 AATCACTTGTCTTGGG 40 2252
    881236 1898 1913 20015 20030 TCAATGATGGCAGTCT 46 2253
    881260 2021 2036 20138 20153 AGTCAGTGTCAATACT 53 2254
    881284 2157 2172 20274 20289 ACTCAGCAAGTGTCTT 53 2255
    881308 2341 2356 20458 20473 GCTCATGTTTTTTGAC 44 2256
    881332 2469 2484 20586 20601 CTTTATGCGAAGAATT 70 2257
    881356 2587 2602 20704 20719 CGCTGGACAGCCAAAC 59 2258
    881380 2780 2795 20897 20912 GCCAAGTAATTTTAAG 65 2259
    881404 2850 2865 20967 20982 ATGTAAGTGATAGGTA 30 2260
    881428 2995 3010 21112 21127 TATCCATTAGAAAAGC 37 2261
    881452 3255 3270 21372 21387 TGGACACTTTTAGAGA 28 2262
    881476 3398 3413 21515 21530 CAGAACGAGGTAAATC 41 2263
    881500 3487 3502 21604 21619 TGCCCAATACATATCC 41 2264
    881523 3611 3626 21728 21743 GGTAAGGGCCCCGTGA 67 2265
    881547 3835 3850 21952 21967 AAGGAGGTAGTGGCCC 53 2266
    881571 4009 4024 22126 22141 GCCAATTCCACTTTAT 36 2267
    881590 4239 4254 22356 22371 TCCTAGGTTTCAGTTG 52 2268
    881614 4389 4404 22506 22521 GTAACAATACTGTAAG 45 2269
    881638 4524 4539 22641 22656 GGCGGAGCATCAACAA 40 2270
    881662 4595 4610 22712 22727 AACGGAAGTTTACACT 41 2271
    881686 4812 4827 22929 22944 CTGCATCGAGATCAGT 48 2272
    881710 4996 5011 23113 23128 TGAAGCAACACGGGAA 40 2273
    881734 5199 5214 23316 23331 AGCATTATCTACCTCA 22 2274
    881758 N/A N/A 18770 18785 AAGCTAAACTCCTAAG 85 2275
    881782 N/A N/A 18837 18852 TCTAAGGCAAGCTGAA 79 2276
    881805 N/A N/A 4003 4018 CAAGGAGGCGGGCCTT 102 2277
    881827 N/A N/A 4325 4340 GGCTAGGCCACCGCAC 72 2278
    881850 N/A N/A 4633 4648 GAGGACCTCGCCTGCG 102 2279
    881874 N/A N/A 4940 4955 CCGGAAGAAGGCACCT 83 2280
    881898 N/A N/A 5648 5663 GCGCAAAACCCCTCAA 78 2281
    881921 N/A N/A 5763 5778 CGGCACAGGCGCGGAC 96 2282
    881942 N/A N/A 6047 6062 GTAAACTGCCTTAGGG 56 2283
    881966 N/A N/A 6369 6384 AAAGACCCCAGCTATG 77 2284
    881988 N/A N/A 7068 7083 GCTCAGAATGAAGTTA 52 2285
    882012 N/A N/A 7327 7342 AAGACTATTAGATAAG 78 2286
    882036 N/A N/A 7629 7644 GTACAGGACAGGTAAA 75 2287
    882060 N/A N/A 8103 8118 ACCAATGGCAGCACCG 39 2288
    882084 N/A N/A 8347 8362 TATGGCTAAACCTGGC 57 2289
    882107 N/A N/A 8487 8502 CCCTTATTAGACTGAC 33 2290
    882131 N/A N/A 9312 9327 GACCAGGATTCGCCAT 77 2291
    882177 N/A N/A 9850 9865 TGAGTTACCGCATTGC 20 2292
    882200 N/A N/A 10121 10136 ACCATATTGGAAACCA 26 2293
    882224 N/A N/A 10278 10293 TGTTACCGATGCTTCA 51 2294
    882248 N/A N/A 10606 10621 GAAACGAGCCAGTGCA 48 2295
    882272 N/A N/A 11027 11042 GAGCAAAGCAAGTGTC 58 2296
    882296 N/A N/A 11323 11338 GCTCAACCTGGAAGGA 75 2297
    882320 N/A N/A 11541 11556 CTTCTTTATAGTAGGT 80 2298
    882344 N/A N/A 11843 11858 TCACGAGCACCTCAGA 64 2299
    882368 N/A N/A 12111 12126 TTCAACACACTGTCTG 131 2300
    882392 N/A N/A 12386 12401 CTCTTTAAAATATCGC 44 2301
    882415 N/A N/A 12872 12887 AAGCAAGTCGGTCCAC 68 2302
    882438 N/A N/A 13161 13176 TCTAAACCAGCATATT 67 2303
    882482 N/A N/A 14085 14100 AAAAGAGCCGCCACAT 84 2304
    882505 N/A N/A 14321 14336 CATGAAATCCAAGGTA 51 2305
    882529 N/A N/A 14671 14686 AAAAACTTGGGTCACT 119 2306
    882552 N/A N/A 15366 15381 CACCAAGGTCCAGAGT 80 2307
    882599 N/A N/A 15893 15908 TCACACTGCCGTGATC 78 2308
    882622 N/A N/A 16151 16166 AACGAGTTGACACAGG 45 2309
    882646 N/A N/A 16314 16329 GTACATCCTGAAGCCA 74 2310
    882669 N/A N/A 16612 16627 ATCAGAATGTTTCGAC 54 2311
    882693 N/A N/A 16807 16822 CCCCAGGGCCCTCGGT 82 2312
    882717 N/A N/A 17147 17162 CACTATGGTAGGAGTG 112 2313
    882741 N/A N/A 17448 17463 GGGCAACTTTAACCAT 92 2314
    882765 N/A N/A 17699 17714 GAACATTACGAGAGGG 30 2315
    882789 N/A N/A 17945 17960 GGTGTAACTTTTACCT 89 2316
    882813 N/A N/A 18558 18573 GATCATCAACTTCTTT 57 2317
    882836 N/A N/A 18760 18775 CCTAAGTACCTGAAAT 89 2318
    882859 N/A N/A 19203 19218 TCAAATCGACTGCCAC 46 2319
    882883 N/A N/A 19392 19407 GCTCACTATTAAACAG 112 2320
    882902 N/A N/A 9579 9594 CAATAATCTCCCAGCA 63 2321
    882907 N/A N/A 13782 13797 AGATAACGAGGTGCCT 77 2322
    882912 N/A N/A 15773 15788 TTAATTATGCAGAAGC 87 2323
  • TABLE 33
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID: SEQ ID: SEQ ID: IRF4 SEQ
    Compound 1 Start 1 Stop 2 Start 2 Stop (% ID
    Number Site Site Site Site Sequence UTC) NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 26 195
    881095 217 232 5244 5259 TGCCGCTGTCGATCTG 68 2324
    881118 559 574 7877 7892 GGCTCATGGACATCTG 64 2325
    881165 1103 1118 13656 13671 TGGCACAGTCTTTTCG 72 2326
    881189 1341 1356 19458 19473 GGCTAGCAGAGGTTCT 49 2327
    881213 1717 1732 19834 19849 CGCTTTCACTAAAGTC 29 2328
    881237 1900 1915 20017 20032 CATCAATGATGGCAGT 50 2329
    881261 2025 2040 20142 20157 CTCTAGTCAGTGTCAA 41 2330
    881285 2158 2173 20275 20290 CACTCAGCAAGTGTCT 50 2331
    881309 2358 2373 20475 20490 TCCCATCCAAGAGTAG 67 2332
    881333 2470 2485 20587 20602 TCTTTATGCGAAGAAT 58 2333
    881357 2600 2615 20717 20732 CGCCATGGCTGATCGC 47 2334
    881381 2817 2832 20934 20949 GTCTTTGGGATTCTAT 35 2335
    881405 2851 2866 20968 20983 AATGTAAGTGATAGGT 20 2336
    881429 3024 3039 21141 21156 TACTAGGTGCTTGTTG 51 2337
    881453 3256 3271 21373 21388 GTGGACACTTTTAGAG 48 2338
    881477 3400 3415 21517 21532 AGCAGAACGAGGTAAA 30 2339
    881501 3500 3515 21617 21632 AAACACAGTCTGCTGC 65 2340
    881524 3612 3627 21729 21744 AGGTAAGGGCCCCGTG 53 2341
    881548 3836 3851 21953 21968 AAAGGAGGTAGTGGCC 79 2342
    881572 4022 4037 22139 22154 TAAATTCTAGTTTGCC 32 2343
    881591 4258 4273 22375 22390 CGCTCAGGACTCAGGG 45 2344
    881615 4390 4405 22507 22522 GGTAACAATACTGTAA 41 2345
    881639 4525 4540 22642 22657 TGGCGGAGCATCAACA 63 2346
    881663 4596 4611 22713 22728 GAACGGAAGTTTACAC 33 2347
    881687 4817 4832 22934 22949 TCCACCTGCATCGAGA 53 2348
    881711 4997 5012 23114 23129 TTGAAGCAACACGGGA 39 2349
    881735 5202 5217 23319 23334 CATAGCATTATCTACC 57 2350
    881759 N/A N/A 18772 18787 TTAAGCTAAACTCCTA 90 2351
    881783 N/A N/A 18840 18855 GCATCTAAGGCAAGCT 66 2352
    881806 N/A N/A 4006 4021 AGCCAAGGAGGCGGGC 101 2353
    881828 N/A N/A 4334 4349 CGCCAGGCCGGCTAGG 90 2354
    881851 N/A N/A 4636 4651 GCGGAGGACCTCGCCT 92 2355
    881875 N/A N/A 4942 4957 CCCCGGAAGAAGGCAC 64 2356
    881899 N/A N/A 5654 5669 ACGAACGCGCAAAACC 94 2357
    881922 N/A N/A 5769 5784 AGCCGCCGGCACAGGC 99 2358
    881943 N/A N/A 6048 6063 GGTAAACTGCCTTAGG 75 2359
    881967 N/A N/A 6371 6386 TGAAAGACCCCAGCTA 96 2360
    881989 N/A N/A 7080 7095 CTAGAAAGTGATGCTC 61 2361
    882013 N/A N/A 7332 7347 CACTAAAGACTATTAG 95 2362
    882037 N/A N/A 7631 7646 TTGTACAGGACAGGTA 72 2363
    882061 N/A N/A 8109 8124 ATCCACACCAATGGCA 66 2364
    882108 N/A N/A 8494 8509 AGGGAATCCCTTATTA 94 2365
    882132 N/A N/A 9317 9332 GGACAGACCAGGATTC 75 2366
    882154 N/A N/A 9580 9595 TCAATAATCTCCCAGC 45 2367
    882178 N/A N/A 9853 9868 GCCTGAGTTACCGCAT 30 2368
    882201 N/A N/A 10122 10137 TACCATATTGGAAACC 52 2369
    882225 N/A N/A 10283 10298 TTTACTGTTACCGATG 52 2370
    882249 N/A N/A 10608 10623 GAGAAACGAGCCAGTG 61 2371
    882273 N/A N/A 11048 11063 ATCTACTCCAGACCCC 73 2372
    882297 N/A N/A 11324 11339 GGCTCAACCTGGAAGG 71 2373
    882321 N/A N/A 11552 11567 CCTAGAGGTGCCTTCT 59 2374
    882345 N/A N/A 11846 11861 TACTCACGAGCACCTC 59 2375
    882369 N/A N/A 12114 12129 TGCTTCAACACACTGT 97 2376
    882393 N/A N/A 12432 12447 TAAACAAGATGAATCC 56 2377
    882416 N/A N/A 12875 12890 AAGAAGCAAGTCGGTC 45 2378
    882439 N/A N/A 13162 13177 GTCTAAACCAGCATAT 81 2379
    882461 N/A N/A 13783 13798 CAGATAACGAGGTGCC 70 2380
    882483 N/A N/A 14086 14101 GAAAAGAGCCGCCACA 93 2381
    882506 N/A N/A 14331 14346 GCTGAATTGTCATGAA 64 2382
    882553 N/A N/A 15369 15384 TGGCACCAAGGTCCAG 99 2383
    882576 N/A N/A 15776 15791 TCCTTAATTATGCAGA 56 2384
    882600 N/A N/A 15895 15910 ATTCACACTGCCGTGA 66 2385
    882623 N/A N/A 16152 16167 AAACGAGTTGACACAG 80 2386
    882670 N/A N/A 16646 16661 CAATTTATGCCATGGA 38 2387
    882694 N/A N/A 16838 16853 TAGCATGTATGCATTC 48 2388
    882718 N/A N/A 17150 17165 AGCCACTATGGTAGGA 57 2389
    882742 N/A N/A 17471 17486 ATCTTAACCTGGAGAA 72 2390
    882766 N/A N/A 17703 17718 TAGAGAACATTACGAG 40 2391
    882790 N/A N/A 17976 17991 CTAGAACATGATGAGA 71 2392
    882837 N/A N/A 18921 18936 TTATACTGTCTGGTTA 56 2393
    882860 N/A N/A 19205 19220 TTTCAAATCGACTGCC 69 2394
    882884 N/A N/A 19400 19415 TGCAACTGGCTCACTA 83 2395
    882900 N/A N/A 8350 8365 TCATATGGCTAAACCT 51 2396
    882911 N/A N/A 14672 14687 CAAAAACTTGGGTCAC 80 2397
    882914 N/A N/A 16378 16393 GTAACTTGACTTGAGA 51 2398
    882915 N/A N/A 18567 18582 AGCTGAGCTGATCATC 44 2399
  • TABLE 34
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID: SEQ ID: SEQ ID: IRF4 SEQ
    Compound 1 Start 1 Stop 2 Start 2 Stop (% ID
    Number Site Site Site Site Sequence UTC) NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 24 195
    881096 328 343 5355 5370 CCTTGAAGAGCGCGGC 76 2400
    881119 594 609 7912 7927 GAGCGAAGGGTAAGGC 62 2401
    881166 1121 1136 13674 13689 TCCCAGTAGATCCTGC 60 2402
    881190 1354 1369 19471 19486 AATATAGTTGTCTGGC 50 2403
    881214 1732 1747 19849 19864 GGGCAGTCAATTGGAC 75 2404
    881238 1903 1918 20020 20035 GATCATCAATGATGGC 37 2405
    881262 2033 2048 20150 20165 AGTCATCACTCTAGTC 47 2406
    881286 2189 2204 20306 20321 GGCACGGCTTCAGTCA 25 2407
    881310 2366 2381 20483 20498 CAAAAATGTCCCATCC 81 2408
    881334 2471 2486 20588 20603 TTCTTTATGCGAAGAA 91 2409
    881358 2609 2624 20726 20741 CTTTAGTGTCGCCATG 71 2410
    881382 2822 2837 20939 20954 TGGAGGTCTTTGGGAT 42 2411
    881406 2882 2897 20999 21014 GTCTACTGCTGTACTT 48 2412
    881430 3025 3040 21142 21157 TTACTAGGTGCTTGTT 50 2413
    881454 3258 3273 21375 21390 TTGTGGACACTTTTAG 51 2414
    881478 3401 3416 21518 21533 GAGCAGAACGAGGTAA 45 2415
    881502 3502 3517 21619 21634 CGAAACACAGTCTGCT 47 2416
    881525 3616 3631 21733 21748 TCACAGGTAAGGGCCC 53 2417
    881549 3837 3852 21954 21969 GAAAGGAGGTAGTGGC 77 2418
    881573 4023 4038 22140 22155 CTAAATTCTAGTTTGC 79 2419
    881592 4276 4291 22393 22408 GACTAACTCTCCTGTT 83 2420
    881616 4391 4406 22508 22523 TGGTAACAATACTGTA 35 2421
    881640 4533 4548 22650 22665 GGCCTTCCTGGCGGAG 78 2422
    881664 4598 4613 22715 22730 ATGAACGGAAGTTTAC 46 2423
    881688 4828 4843 22945 22960 TCTCAAGGAGATCCAC 99 2424
    881712 4998 5013 23115 23130 TTTGAAGCAACACGGG 53 2425
    881736 5203 5218 23320 23335 GCATAGCATTATCTAC 49 2426
    881760 N/A N/A 18774 18789 ACTTAAGCTAAACTCC 79 2427
    881784 N/A N/A 18841 18856 AGCATCTAAGGCAAGC 43 2428
    881807 N/A N/A 4042 4057 CAGGAGCGCGGAGGGC 89 2429
    881829 N/A N/A 4367 4382 ACGACAGCTGCGGAGC 73 2430
    881852 N/A N/A 4638 4653 GCGCGGAGGACCTCGC 90 2431
    881876 N/A N/A 5008 5023 GACCACGAGGCCCCGG 69 2432
    881900 N/A N/A 5656 5671 GGACGAACGCGCAAAA 65 2433
    881923 N/A N/A 5773 5788 AAACAGCCGCCGGCAC 89 2434
    881944 N/A N/A 6117 6132 TCCCGGAGGAAGTCCC 70 2435
    881968 N/A N/A 6377 6392 GTAAACTGAAAGACCC 65 2436
    881990 N/A N/A 7152 7167 CATAACTCAGGCAAGG 64 2437
    882014 N/A N/A 7335 7350 ACTCACTAAAGACTAT 82 2438
    882038 N/A N/A 7645 7660 CTACAAGGTCTGAGTT 83 2439
    882062 N/A N/A 8116 8131 ACTTAAAATCCACACC 93 2440
    882085 N/A N/A 8366 8381 TTTATGTAAAGCTTCG 25 2441
    882109 N/A N/A 8498 8513 CCTCAGGGAATCCCTT 70 2442
    882133 N/A N/A 9340 9355 GGAAAGAGCTTTGGTG 88 2443
    882155 N/A N/A 9581 9596 CTCAATAATCTCCCAG 47 2444
    882179 N/A N/A 9877 9892 GTAACTAACTCAAAAG 101 2445
    882202 N/A N/A 10125 10140 CACTACCATATTGGAA 78 2446
    882226 N/A N/A 10284 10299 ATTTACTGTTACCGAT 71 2447
    882250 N/A N/A 10609 10624 GGAGAAACGAGCCAGT 53 2448
    882274 N/A N/A 11052 11067 CTACATCTACTCCAGA 78 2449
    882298 N/A N/A 11332 11347 TTATTTGTGGCTCAAC 82 2450
    882322 N/A N/A 11554 11569 AGCCTAGAGGTGCCTT 59 2451
    882346 N/A N/A 11859 11874 GGGCATCCTCAGTTAC 67 2452
    882370 N/A N/A 12138 12153 ACCCACATCACTGTCT 85 2453
    882394 N/A N/A 12456 12471 CTAAAACTGCGCTCTC 76 2454
    882417 N/A N/A 12878 12893 AGAAAGAAGCAAGTCG 63 2455
    882440 N/A N/A 13169 13184 TTAATCTGTCTAAACC 84 2456
    882462 N/A N/A 13784 13799 ACAGATAACGAGGTGC 70 2457
    882484 N/A N/A 14116 14131 TTCCAACCTTTATGAT 93 2458
    882507 N/A N/A 14335 14350 GTTCGCTGAATTGTCA 63 2459
    882530 N/A N/A 14674 14689 TACAAAAACTTGGGTC 91 2460
    882554 N/A N/A 15406 15421 TAGAAAGCCCTCACCT 95 2461
    882577 N/A N/A 15781 15796 GGGAATCCTTAATTAT 88 2462
    882601 N/A N/A 15898 15913 TACATTCACACTGCCG 42 2463
    882624 N/A N/A 16154 16169 AGAAACGAGTTGACAC 85 2464
    882647 N/A N/A 16380 16395 CAGTAACTTGACTTGA 61 2465
    882671 N/A N/A 16647 16662 CCAATTTATGCCATGG 88 2466
    882695 N/A N/A 16857 16872 GAACATCTCAGATACA 58 2467
    882719 N/A N/A 17158 17173 GAACAGGAAGCCACTA 77 2468
    882743 N/A N/A 17481 17496 TCTTACAGCAATCTTA 68 2469
    882767 N/A N/A 17709 17724 CTATGCTAGAGAACAT 77 2470
    882791 N/A N/A 17977 17992 GCTAGAACATGATGAG 86 2471
    882814 N/A N/A 18570 18585 GATAGCTGAGCTGATC 68 2472
    882838 N/A N/A 18923 18938 ATTTATACTGTCTGGT 51 2473
    882861 N/A N/A 19211 19226 TGTTACTTTCAAATCG 52 2474
    882885 N/A N/A 19401 19416 CTGCAACTGGCTCACT 90 2475
  • TABLE 35
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID: SEQ ID: SEQ ID: IRF4 SEQ
    Compound 1 Start 1 Stop 2 Start 2 Stop (% ID
    Number Site Site Site Site Sequence UTC) NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 12 195
    881097 329 344 N/A N/A GCCTTGAAGAGCGCGG 91 2476
    881120 613 628 N/A N/A TGTGAACCTGCTGGGC 98 2477
    881167 1189 1204 13742 13757 CAAAGAGCTTGCAGGT 96 2478
    881191 1355 1370 19472 19487 TAATATAGTTGTCTGG 60 2479
    881215 1738 1753 19855 19870 GTAAGAGGGCAGTCAA 56 2480
    881239 1910 1925 20027 20042 TCACAGTGATCATCAA 57 2481
    881263 2040 2055 20157 20172 TACAAGCAGTCATCAC 71 2482
    881287 2190 2205 20307 20322 AGGCACGGCTTCAGTC 51 2483
    881311 2382 2397 20499 20514 TAGATTGTAGGACAGA 72 2484
    881335 2472 2487 20589 20604 CTTCTTTATGCGAAGA 105 2485
    881359 2610 2625 20727 20742 CCTTTAGTGTCGCCAT 42 2486
    881383 2824 2839 20941 20956 AGTGGAGGTCTTTGGG 45 2487
    881407 2887 2902 21004 21019 CCCCAGTCTACTGCTG 53 2488
    881431 3026 3041 21143 21158 CTTACTAGGTGCTTGT 62 2489
    881455 3270 3285 21387 21402 AAACACCCCTTCTTGT 113 2490
    881479 3404 3419 21521 21536 TCTGAGCAGAACGAGG 53 2491
    881503 3503 3518 21620 21635 ACGAAACACAGTCTGC 48 2492
    881526 3618 3633 21735 21750 GGTCACAGGTAAGGGC 75 2493
    881550 3896 3911 22013 22028 TCATACCCTGGATCAC 57 2494
    881574 4039 4054 22156 22171 GTCCACTGAGTACAAA 87 2495
    881593 4278 4293 22395 22410 GCGACTAACTCTCCTG 30 2496
    881617 4410 4425 22527 22542 AATACCTACCTGCCCT 85 2497
    881641 4540 4555 22657 22672 CACAAGTGGCCTTCCT 55 2498
    881665 4600 4615 22717 22732 CAATGAACGGAAGTTT 67 2499
    881689 4837 4852 22954 22969 CTATCAGGATCTCAAG 91 2500
    881713 5020 5035 23137 23152 TGTTAAGTCCCATCTG 75 2501
    881737 5204 5219 23321 23336 AGCATAGCATTATCTA 66 2502
    881761 N/A N/A 18775 18790 GACTTAAGCTAAACTC 42 2503
    881785 N/A N/A 18842 18857 CAGCATCTAAGGCAAG 46 2504
    881830 N/A N/A 4368 4383 GACGACAGCTGCGGAG 55 2505
    881853 N/A N/A 4640 4655 ACGCGCGGAGGACCTC 87 2506
    881877 N/A N/A 5011 5026 AGTGACCACGAGGCCC 85 2507
    881901 N/A N/A 5657 5672 CGGACGAACGCGCAAA 61 2508
    881924 N/A N/A 5775 5790 GAAAACAGCCGCCGGC 74 2509
    881945 N/A N/A 6122 6137 CAAATTCCCGGAGGAA 95 2510
    881969 N/A N/A 6378 6393 CGTAAACTGAAAGACC 52 2511
    881991 N/A N/A 7153 7168 ACATAACTCAGGCAAG 99 2512
    882015 N/A N/A 7345 7360 CAAAATAGTCACTCAC 103 2513
    882039 N/A N/A 7646 7661 TCTACAAGGTCTGAGT 43 2514
    882063 N/A N/A 8119 8134 CCAACTTAAAATCCAC 91 2515
    882086 N/A N/A 8380 8395 GATACTTGTACTGTTT 22 2516
    882110 N/A N/A 8546 8561 AAGAAGCACTGGCATT 78 2517
    9066 9081
    882134 N/A N/A 9341 9356 GGGAAAGAGCTTTGGT 95 2518
    882156 N/A N/A 9592 9607 AAATATACCAGCTCAA 75 2519
    882180 N/A N/A 9921 9936 CCAAAGGGTTCAGTGT 74 2520
    882203 N/A N/A 10128 10143 CTCCACTACCATATTG 99 2521
    882227 N/A N/A 10285 10300 CATTTACTGTTACCGA 21 2522
    882251 N/A N/A 10610 10625 TGGAGAAACGAGCCAG 62 2523
    882275 N/A N/A 11054 11069 GTCTACATCTACTCCA 62 2524
    882299 N/A N/A 11333 11348 CTTATTTGTGGCTCAA 45 2525
    882323 N/A N/A 11655 11670 ACCTTAAGCTATTTGG 39 2526
    882347 N/A N/A 11865 11880 CCCAAAGGGCATCCTC 59 2527
    882371 N/A N/A 12143 12158 ACTTAACCCACATCAC 122 2528
    882395 N/A N/A 12484 12499 GGCTTTGTGTTTAAGT 77 2529
    882418 N/A N/A 12890 12905 TAACGGTGTTTCAGAA 74 2530
    882441 N/A N/A 13173 13188 CCATTTAATCTGTCTA 72 2531
    882463 N/A N/A 13785 13800 AACAGATAACGAGGTG 104 2532
    882485 N/A N/A 14124 14139 CAATATGCTTCCAACC 115 2533
    882508 N/A N/A 14343 14358 AGCCAGAGGTTCGCTG 75 2534
    882531 N/A N/A 14677 14692 GCTTACAAAAACTTGG 74 2535
    882555 N/A N/A 15407 15422 TTAGAAAGCCCTCACC 116 2536
    882578 N/A N/A 15782 15797 TGGGAATCCTTAATTA 88 2537
    882625 N/A N/A 16155 16170 AAGAAACGAGTTGACA 78 2538
    882648 N/A N/A 16385 16400 TGGAACAGTAACTTGA 88 2539
    882672 N/A N/A 16648 16663 ACCAATTTATGCCATG 83 2540
    882696 N/A N/A 16860 16875 TGTGAACATCTCAGAT 88 2541
    882720 N/A N/A 17170 17185 GGCCTTTACAAAGAAC 119 2542
    882744 N/A N/A 17487 17502 TAGCATTCTTACAGCA 43 2543
    882768 N/A N/A 17726 17741 GTTGAACCCATCTTGA 84 2544
    882792 N/A N/A 17978 17993 AGCTAGAACATGATGA 95 2545
    882815 N/A N/A 18571 18586 TGATAGCTGAGCTGAT 63 2546
    882839 N/A N/A 18939 18954 AGCTAACTGGCCTCAA 77 2547
    882862 N/A N/A 19221 19236 GGGTTAAAGATGTTAC 50 2548
    882886 N/A N/A 19408 19423 AGATATCCTGCAACTG 109 2549
    882891 N/A N/A 4045 4060 TCGCAGGAGCGCGGAG 137 2550
    882913 N/A N/A 15899 15914 ATACATTCACACTGCC 55 2551
  • TABLE 36
    Percent control of human IRF4 mRNA with 3-10-3 cEt gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID: SEQ ID: SEQ ID: IRF4 SEQ
    Compound 1 Start 1 Stop 2 Start 2 Stop (% ID
    Number Site Site Site Site Sequence UTC) NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT 26 195
    881098 335 350 N/A N/A GCCCAAGCCTTGAAGA 85 2552
    881121 620 635 9110 9125 ATGTAGTTGTGAACCT 61 2553
    881168 1191 1206 13744 13759 GTCAAAGAGCTTGCAG 56 2554
    881192 1356 1371 19473 19488 ATAATATAGTTGTCTG 65 2555
    881216 1739 1754 19856 19871 AGTAAGAGGGCAGTCA 50 2556
    881240 1919 1934 20036 20051 GGTCAATTTTCACAGT 36 2557
    881264 2041 2056 20158 20173 CTACAAGCAGTCATCA 56 2558
    881288 2192 2207 20309 20324 ACAGGCACGGCTTCAG 36 2559
    881312 2384 2399 20501 20516 ACTAGATTGTAGGACA 109 2560
    881336 2507 2522 20624 20639 GTTCAAGTATTAAGAT 71 2561
    881360 2611 2626 20728 20743 TCCTTTAGTGTCGCCA 24 2562
    881384 2825 2840 20942 20957 AAGTGGAGGTCTTTGG 34 2563
    881432 3043 3058 21160 21175 TAGGGATACAGCAGGC 27 2564
    881456 3272 3287 21389 21404 ATAAACACCCCTTCTT 70 2565
    881480 3408 3423 21525 21540 GGCCTCTGAGCAGAAC 73 2566
    881504 3504 3519 21621 21636 CACGAAACACAGTCTG 48 2567
    881527 3624 3639 21741 21756 AAAGAGGGTCACAGGT 66 2568
    881551 3898 3913 22015 22030 GGTCATACCCTGGATC 51 2569
    881575 4051 4066 22168 22183 TTCAACAGCACTGTCC 35 2570
    881594 4284 4299 22401 22416 TGTAGGGCGACTAACT 79 2571
    881618 4411 4426 22528 22543 TAATACCTACCTGCCC 96 2572
    881642 4543 4558 22660 22675 ACACACAAGTGGCCTT 56 2573
    881666 4601 4616 22718 22733 GCAATGAACGGAAGTT 55 2574
    881690 4838 4853 22955 22970 GCTATCAGGATCTCAA 62 2575
    881714 5021 5036 23138 23153 CTGTTAAGTCCCATCT 46 2576
    881738 5205 5220 23322 23337 CAGCATAGCATTATCT 151 2577
    881762 N/A N/A 18777 18792 ACGACTTAAGCTAAAC 42 2578
    881786 N/A N/A 18846 18861 TTTACAGCATCTAAGG 66 2579
    881808 N/A N/A 4055 4070 GGCGACCCCGTCGCAG 70 2580
    881831 N/A N/A 4372 4387 GGGCGACGACAGCTGC 68 2581
    881854 N/A N/A 4642 4657 CCACGCGCGGAGGACC 81 2582
    881878 N/A N/A 5015 5030 CGCCAGTGACCACGAG 58 2583
    881902 N/A N/A 5659 5674 CACGGACGAACGCGCA 102 2584
    881946 N/A N/A 6124 6139 ACCAAATTCCCGGAGG 93 2585
    881970 N/A N/A 6413 6428 GCATAGGTCCTTCAGA 69 2586
    881992 N/A N/A 7154 7169 CACATAACTCAGGCAA 63 2587
    882016 N/A N/A 7347 7362 TGCAAAATAGTCACTC 52 2588
    882040 N/A N/A 7647 7662 TTCTACAAGGTCTGAG 53 2589
    882064 N/A N/A 8139 8154 GCGGACACGCCCGACC 85 2590
    882087 N/A N/A 8383 8398 GGAGATACTTGTACTG 34 2591
    882111 N/A N/A 8550 8565 AGATAAGAAGCACTGG 75 2592
    8706 8721
    8810 8825
    8966 8981
    9070 9085
    882157 N/A N/A 9593 9608 GAAATATACCAGCTCA 39 2593
    882181 N/A N/A 9957 9972 GGCCAAATTGCAAAGG 52 2594
    882204 N/A N/A 10149 10164 TAGTTTTATGTTAGCC 25 2595
    882228 N/A N/A 10287 10302 TTCATTTACTGTTACC 29 2596
    882252 N/A N/A 10615 10630 GCTGATGGAGAAACGA 93 2597
    882276 N/A N/A 11087 11102 TAAATCACCCTGGTCA 78 2598
    882300 N/A N/A 11347 11362 GTAGAGGAGGAGGACT 84 2599
    882324 N/A N/A 11660 11675 TCCAAACCTTAAGCTA 63 2600
    882348 N/A N/A 11891 11906 AGCCTTCCTGCTCAGA 45 2601
    882372 N/A N/A 12144 12159 GACTTAACCCACATCA 266 2602
    882396 N/A N/A 12492 12507 TCCCACTGGGCTTTGT 68 2603
    882419 N/A N/A 12891 12906 ATAACGGTGTTTCAGA 53 2604
    882442 N/A N/A 13174 13189 CCCATTTAATCTGTCT 67 2605
    882464 N/A N/A 13787 13802 CTAACAGATAACGAGG 77 2606
    882486 N/A N/A 14129 14144 GTTAACAATATGCTTC 75 2607
    882509 N/A N/A 14347 14362 AGCCAGCCAGAGGTTC 70 2608
    882532 N/A N/A 14691 14706 GAAAATCTGGATGAGC 36 2609
    882556 N/A N/A 15437 15452 AGCCAGTGCCAGTTCC 61 2610
    882579 N/A N/A 15803 15818 AGATAACATGAGAGTG 59 2611
    882602 N/A N/A 15923 15938 AATGACTTAGTCAGAA 73 2612
    882626 N/A N/A 16159 16174 GCAAAAGAAACGAGTT 92 2613
    882649 N/A N/A 16387 16402 GATGGAACAGTAACTT 49 2614
    882673 N/A N/A 16663 16678 ACGCAATGGCAAAAGA 89 2615
    882697 N/A N/A 16887 16902 TCTTACTCCGCTGAGT 65 2616
    882721 N/A N/A 17224 17239 TTCCAGGTCATTTGAC 34 2617
    882745 N/A N/A 17492 17507 CTAGATAGCATTCTTA 61 2618
    882769 N/A N/A 17731 17746 CCACAGTTGAACCCAT 64 2619
    882793 N/A N/A 17982 17997 TCAGAGCTAGAACATG 62 2620
    882816 N/A N/A 18579 18594 GATTGATGTGATAGCT 44 2621
    882840 N/A N/A 18960 18975 CTACTATTGTGGAAAA 97 2622
    882863 N/A N/A 19230 19245 CTTAATTCTGGGTTAA 47 2623
    882887 N/A N/A 19417 19432 ACATTACTGAGATATC 84 2624
    882895 N/A N/A 5776 5791 CGAAAACAGCCGCCGG 85 2625
    882901 N/A N/A 9358 9373 ACGCAGCCTCTAAGAA 75 2626
  • Example 7: Effect of Mixed MOE and cEt Gapmers with Phosphorothioate Internucleoside Linkages on Human IRF4 In Vitro, Single Dose
  • Modified oligonucleotides complementary to a human IRF4 nucleic acid were designed and tested for their effect on IRF4 mRNA in vitro.
  • Cultured MM.1R cells at a density of 5,000 cells per well were transfected by free uptake with 1,000 nM concentration of modified oligonucleotide or no modified oligonucleotide for untreated controls. After approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by quantitative real-time PCR. Human primer probe set hIRF4_LTS34726 (forward sequence GGCAAAGAAAGCTCATCACAG, designated herein as SEQ ID NO: 3389; reverse sequence GGATTGCTGATGTGTTCTGGTA designated herein as SEQ ID NO: 3390; probe sequence TAGCCCCTCAGGAAATGTCCACTG, designated herein as SEQ ID: 3391) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN®. Results are presented in the table below as percent control of the amount of IRF4 mRNA, relative to untreated control (UTC) cells.
  • The modified oligonucleotides in Table 37 are cEt and/or MOE containing gapmers. The modified oligonucleotides have a central gap segment comprising 2′-deoxynucleosides which is flanked by wing segments on the 5′ direction and the 3′ direction. At least one nucleoside in the 5′ wing segment and/or one nucleoside in the 3′ wing segment has a MOE and/or cEt sugar modification. The “Motif” column describes the sugar modifications of each oligonucleotide. “k” indicates a cEt sugar modification; “d” indicates deoxyribose; and “e” indicates a MOE modification. Each internucleoside linkage is a phosphorothioate internucleoside linkage and each cytosine residue is a 5-methylcytosine. “Start Site” indicates the 5′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence. “Stop Site” indicates the 3′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Each modified oligonucleotide listed in Table 37 below is complementary to human IRF4 nucleic acid sequences SEQ ID NO: 1 or SEQ ID NO: 2, as indicated. ‘N/A’ indicates that the modified oligonucleotide is not complementary to that particular nucleic acid sequence with 100% complementarity. As shown below, modified oligonucleotides complementary to human IRF4 reduced the amount of human IRF4 mRNA.
  • TABLE 35
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ SEQ SEQ SEQ
    ID: 1 ID: 1 ID: 2 ID: 2 IRF4 SEQ
    Compound Start Stop Start Stop (% ID
    Number Site Site Site Site Sequence Motif UTC) NO
    881450 3252 3267 21369 21384 ACACTTTTAGAGAGGA kkk-d10-kkk 47 2111
    881659 4592 4607 22709 22724 GGAAGTTTACACTGGA kkk-d10-kkk 15 2044
    935895 4200 4215 22317 22332 TCTATAGTGTTCCAGG kk-d9-ecckk 50 1734
    935896 3070 3085 21187 21202 GCTTGATAAAGGCTGA kk-d9-eeekk 72 1505
    935897 3251 3266 21368 21383 CACTTTTAGAGAGGAG kk-d9-eeekk 67 2036
    935898 4227 4242 22344 22359 GTTGTAAATGAGTCGG kk-d9-eeekk 18 559
    935899 4591 4606 22708 22723 GAAGTTTACACTGGAT kk-d9-eeekk 72 1968
    935900 N/A N/A 8464 8479 GCATTTTATCATCCGA kk-d9-eeekk 62 1605
    935901 N/A N/A 11115 11130 GTGATGTCAGGTTTTC kk-d9-eeekk 62 2627
    935902 5186 5201 23303 23318 TCAGTTTGTGAAGCAT kk-d9-eeekk 61 649
    935903 4171 4186 22288 22303 TGCTTGAGGTTTTCCT kk-d9-eeekk 68 548
    935904 2914 2929 21031 21046 AGTATGAGAAACGGCC kk-d9-eeekk 84 1045
    935905 4199 4214 22316 22331 CTATAGTGTTCCAGGA kk-d9-eeekk 66 552
    935906 3069 3084 21186 21201 CTTGATAAAGGCTGAA kk-d9-eeekk 90 1427
    935907 3250 3265 21367 21382 ACTTTTAGAGAGGAGA kk-d9-eeekk 64 1960
    935908 4226 4241 22343 22358 TTGTAAATGAGTCGGT kk-d9-eeekk 52 195
    935909 4593 4608 22710 22725 CGGAAGTTTACACTGG kk-d9-eeekk 66 2119
    935910 N/A N/A 8466 8481 AAGCATTTTATCATCC kk-d9-eeekk 79 2628
    935911 N/A N/A 11117 11132 CAGTGATGTCAGGTTT kk-d9-eeekk 44 2629
    935912 5188 5203 23305 23320 CCTCAGTTTGTGAAGC kk-d9-eeekk 67 1894
    935913 4173 4188 22290 22305 ACTGCTTGAGGTTTTC kk-d9-eeekk 55 1356
    935914 2916 2931 21033 21048 GTAGTATGAGAAACGG kk-d9-eeekk 49 426
    935915 4201 4216 22318 22333 CTCTATAGTGTTCCAG kk-d9-eeekk 52 1811
    935916 3071 3086 21188 21203 AGCTTGATAAAGGCTG kk-d9-eeekk 97 1579
    935917 3252 3267 21369 21384 ACACTTTTAGAGAGGA kk-d9-eeekk 79 2111
    935918 4228 4243 22345 22360 AGTTGTAAATGAGTCG kk-d9-eeekk 34 2021
    935919 4594 4609 22711 22726 ACGGAAGTTTACACTG kk-d9-eeekk 85 2195
    935920 N/A N/A 8467 8482 GAAGCATTTTATCATC kk-d9-eeekk 91 2630
    935921 N/A N/A 11118 11133 GCAGTGATGTCAGGTT kk-d9-eeekk 19 2631
    935922 5189 5204 23306 23321 ACCTCAGTTTGTGAAG kk-d9-eeekk 96 1971
    935923 4174 4189 22291 22306 TACTGCTTGAGGTTTT kk-d9-eeekk 90 1433
    935924 2917 2932 21034 21049 TGTAGTATGAGAAACG kk-d9-eeekk 93 1197
    935925 4202 4217 22319 22334 TCTCTATAGTGTTCCA kk-d9-eeekk 43 2632
    935926 3072 3087 21189 21204 AAGCTTGATAAAGGCT kk-d9-eeekk 47 2633
    935927 3253 3268 21370 21385 GACACTTTTAGAGAGG kk-d9-eeekk 75 451
    935928 4229 4244 22346 22361 CAGTTGTAAATGAGTC kk-d9-eeekk 38 560
    935929 4592 4607 22709 22724 GGAAGTTTACACTGGA kk-d9-ekeke 36 2044
    935930 N/A N/A 8465 8480 AGCATTTTATCATCCG kk-d9-ekeke 54 1679
    935931 N/A N/A 11116 11131 AGTGATGTCAGGTTTT kk-d9-ekeke 67 1232
    935932 5187 5202 23304 23319 CTCAGTTTGTGAAGCA kk-d9-ekeke 72 1817
    935933 4172 4187 22289 22304 CTGCTTGAGGTTTTCC kk-d9-ekeke 51 1279
    935934 2915 2930 21032 21047 TAGTATGAGAAACGGC kk-d9-ekeke 50 1121
    935935 4200 4215 22317 22332 TCTATAGTGTTCCAGG kk-d9-ekeke 44 1734
    935936 3070 3085 21187 21202 GCTTGATAAAGGCTGA kk-d9-ekeke 61 1505
    935937 3251 3266 21368 21383 CACTTTTAGAGAGGAG kk-d9-ekeke 74 2036
    935938 4227 4242 22344 22359 GTTGTAAATGAGTCGG kk-d9-ekeke 52 559
    935939 4591 4606 22708 22723 GAAGTTTACACTGGAT kk-d9-ekeke 42 1968
    935940 N/A N/A 8464 8479 GCATTTTATCATCCGA kk-d9-ekeke 56 1605
    935941 N/A N/A 11115 11130 GTGATGTCAGGTTTTC kk-d9-ekeke 42 2627
    935942 5186 5201 23303 23318 TCAGTTTGTGAAGCAT kk-d9-ekeke 55 649
    935943 4171 4186 22288 22303 TGCTTGAGGTTTTCCT kk-d9-ekeke 55 548
    935944 2914 2929 21031 21046 AGTATGAGAAACGGCC kk-d9-ekeke 89 1045
    935945 4199 4214 22316 22331 CTATAGTGTTCCAGGA kk-d9-ekeke 52 552
    935946 3069 3084 21186 21201 CTTGATAAAGGCTGAA kk-d9-ekeke 81 1427
    935947 3250 3265 21367 21382 ACTTTTAGAGAGGAGA kk-d9-ekeke 48 1960
    935948 4226 4241 22343 22358 TTGTAAATGAGTCGGT kk-d9-ekeke 43 195
    935949 4593 4608 22710 22725 CGGAAGTTTACACTGG kk-d9-ekeke 67 2119
    935950 N/A N/A 8466 8481 AAGCATTTTATCATCC kk-d9-ekeke 75 2628
    935951 N/A N/A 11117 11132 CAGTGATGTCAGGTTT kk-d9-ekeke 53 2629
    935952 5188 5203 23305 23320 CCTCAGTTTGTGAAGC kk-d9-ekeke 79 1894
    935953 4173 4188 22290 22305 ACTGCTTGAGGTTTTC kk-d9-ekeke 60 1356
    935954 2916 2931 21033 21048 GTAGTATGAGAAACGG kk-d9-ekeke 65 426
    935955 4201 4216 22318 22333 CTCTATAGTGTTCCAG kk-d9-ekeke 57 1811
    935956 3071 3086 21188 21203 AGCTTGATAAAGGCTG kk-d9-ekeke 82 1579
    935957 3252 3267 21369 21384 ACACTTTTAGAGAGGA kk-d9-ekeke 59 2111
    935958 4228 4243 22345 22360 AGTTGTAAATGAGTCG kk-d9-ekeke 27 2021
    935959 4594 4609 22711 22726 ACGGAAGTTTACACTG kk-d9-ekeke 92 2195
    935960 N/A N/A 8467 8482 GAAGCATTTTATCATC kk-d9-ekeke 94 2630
    935961 N/A N/A 11118 11133 GCAGTGATGTCAGGTT kk-d9-ekeke 20 2631
    935962 5189 5204 23306 23321 ACCTCAGTTTGTGAAG kk-d9-ekeke 87 1971
    935963 4174 4189 22291 22306 TACTGCTTGAGGTTTT kk-d9-ekeke 82 1433
    935964 2917 2932 21034 21049 TGTAGTATGAGAAACG kk-d9-ekeke 87 1197
    935965 4202 4217 22319 22334 TCTCTATAGTGTTCCA kk-d9-ekeke 61 2632
    935966 3072 3087 21189 21204 AAGCTTGATAAAGGCT kk-d9-ekeke 62 2633
    935967 3253 3268 21370 21385 GACACTTTTAGAGAGG kk-d9-ekeke 78 451
    935968 4229 4244 22346 22361 CAGTTGTAAATGAGTC kk-d9-ekeke 28 560
    935969 4592 4607 22709 22724 GGAAGTTTACACTGGA k-d9-kekeke 68 2044
    935970 N/A N/A 8465 8480 AGCATTTTATCATCCG k-d9-kekeke 76 1679
  • Example 8: Effect of Mixed MOE and cEt Gapmers with Phosphorothioate Internucleoside Linkages on Human IRF4 In Vitro, Single Dose
  • Modified oligonucleotides complementary to a human IRF4 nucleic acid were designed and tested for their effect on IRF4 mRNA in vitro.
  • Cultured MM.1R cells at a density of 5,000 cells per well were transfected by free uptake with 1,000 nM concentration of modified oligonucleotide or no modified oligonucleotide for untreated controls. After approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by quantitative real-time PCR. Human primer probe set hIRF4_LTS34726 (described hereinabove in Example 7) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN®. Results are presented in the table below as percent control of the amount of IRF4 mRNA, relative to untreated control (UTC) cells.
  • The modified oligonucleotides in Tables 38 through 42 are cEt and/or MOE containing gapmers. The modified oligonucleotides have a central gap segment comprising 2′-deoxynucleosides which is flanked by wing segments on the 5′ direction and the 3′ direction. At least one nucleoside in the 5′ wing segment and/or one nucleoside in the 3′ wing segment has a MOE and/or cEt sugar modification. The “Motif” column describes the sugar modifications of each oligonucleotide. “k” indicates a cEt sugar modification; “d” indicates deoxyribose; and “e” indicates a MOE modification. Each internucleoside linkage is a phosphorothioate internucleoside linkage and each cytosine residue is a 5-methylcytosine. “Start Site” indicates the 5′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence. “Stop Site” indicates the 3′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Each modified oligonucleotide listed in Tables 38 through 42 below is complementary to human IRF4 nucleic acid sequences SEQ ID NO: 1 or SEQ ID NO: 2, as indicated. ‘N/A’ indicates that the modified oligonucleotide is not complementary to that particular nucleic acid sequence with 100% complementarity. As shown below, modified oligonucleotides complementary to human IRF4 reduced the amount of human IRF4 mRNA.
  • TABLE 38
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID: SEQ ID: SEQ ID: IRF4 SEQ
    Compound 1 Start 1 Stop 2 Start 2 Stop (% ID
    Number Site Site Site Site Sequence Motif UTC) NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT kkk-d10-kkk  37  195
    881450 3252 3267 21369 21384 ACACTTTTAGAGAGGA kkk-d10-kkk  53 2111
    881659 4592 4607 22709 22724 GGAAGTTTACACTGGA kkk-d10-kkk  14 2044
    935570 N/A N/A  8455  8470 CATCCGAAAAGACTGG kkk-d10-kkk  86 2634
    935571 N/A N/A  8456  8471 TCATCCGAAAAGACTG kkk-d10-kkk  84 2635
    935572 N/A N/A  8457  8472 ATCATCCGAAAAGACT kkk-d10-kkk  96 2636
    935573 N/A N/A  8458  8473 TATCATCCGAAAAGAC kkk-d10-kkk  97 2637
    935574 N/A N/A  8459  8474 TTATCATCCGAAAAGA kkk-d10-kkk  96 2638
    935575 N/A N/A  8460  8475 TTTATCATCCGAAAAG kkk-d10-kkk  93 2639
    935576 N/A N/A  8472  8487 CAGCCGAAGCATTTTA kkk-d10-kkk 100 2640
    935577 N/A N/A  8473  8488 ACAGCCGAAGCATTTT kkk-d10-kkk  92 2641
    935578 N/A N/A  8474  8489 GACAGCCGAAGCATTT kkk-d10-kkk  94 2642
    935580 N/A N/A 11115 11130 GTGATGTCAGGTTTTC kkk-d10-kkk  34 2627
    935581 N/A N/A 11117 11132 CAGTGATGTCAGGTTT kkk-d10-kkk  38 2629
    935582 N/A N/A 11118 11133 GCAGTGATGTCAGGTT kkk-d10-kkk  61 2631
    935584 N/A N/A 11124 11139 CCACAAGCAGTGATGT kkk-d10-kkk  84 2643
    935585 N/A N/A 11125 11140 ACCACAAGCAGTGATG kkk-d10-kkk  99 2644
    935586 2905 2920 21022 21037 AACGGCCTGGAGGTGA kkk-d10-kkk  99 2645
    935587 2906 2921 21023 21038 AAACGGCCTGGAGGTG kkk-d10-kkk  89 2646
    935588 2907 2922 21024 21039 GAAACGGCCTGGAGGT kkk-d10-kkk  83 2647
    935590 2920 2935 21037 21052 TCCTGTAGTATGAGAA kkk-d10-kkk  78 2648
    935591 2922 2937 21039 21054 TATCCTGTAGTATGAG kkk-d10-kkk  58 2649
    935593 3072 3087 21189 21204 AAGCTTGATAAAGGCT kkk-d10-kkk  97 2633
    935597 3080 3095 21197 21212 TGCTCACTAAGCTTGA kkk-d10-kkk  88 2650
    935603 4178 4193 22295 22310 TAATTACTGCTTGAGG kkk-d10-kkk  38 2651
    935606 4194 4209 22311 22326 GTGTTCCAGGAGATAT kkk-d10-kkk  70 2652
    935608 4196 4211 22313 22328 TAGTGTTCCAGGAGAT kkk-d10-kkk  47 2653
    935611 4208 4223 22325 22340 CTTGGTTCTCTATAGT kkk-d10-kkk  73 2654
    935614 4597 4612 22714 22729 TGAACGGAAGTTTACA kkk-d10-kkk  86 2655
    935616 5190 5205 23307 23322 TACCTCAGTTTGTGAA kkk-d10-kkk  89 2656
    935618 N/A N/A  8466  8481 AAGCATTTTATCATCC kkk-d10-kkk  75 2628
    935619 N/A N/A  8467  8482 GAAGCATTTTATCATC kkk-d10-kkk  96 2630
    935620 4202 4217 22319 22334 TCTCTATAGTGTTCCA kkk-d10-kkk  30 2632
    935621 4592 4607 22709 22724 GGAAGTTTACACTGGA k-d10-kekek  67 2044
    935622 N/A N/A  8465  8480 AGCATTTTATCATCCG k-d10-kekek  64 1679
    935623 N/A N/A 11116 11131 AGTGATGTCAGGTTTT k-d10-kekek  75 1232
    935624 5187 5202 23304 23319 CTCAGTTTGTGAAGCA k-d10-kekek  76 1817
    935625 4172 4187 22289 22304 CTGCTTGAGGTTTTCC k-d10-kekek  92 1279
    935626 2915 2930 21032 21047 TAGTATGAGAAACGGC k-d10-kekek  76 1121
    935627 4200 4215 22317 22332 TCTATAGTGTTCCAGG k-d10-kekek  84 1734
    935628 3070 3085 21187 21202 GCTTGATAAAGGCTGA k-d10-kekek  83 1505
    935629 3251 3266 21368 21383 CACTTTTAGAGAGGAG k-d10-kekek  81 2036
    935630 4591 4606 22708 22723 GAAGTTTACACTGGAT k-d10-kekek  73 1968
    935631 N/A N/A  8464  8479 GCATTTTATCATCCGA k-d10-kekek  79 1605
    935632 N/A N/A 11115 11130 GTGATGTCAGGTTTTC k-d10-kekek  78 2627
    935633 5186 5201 23303 23318 TCAGTTTGTGAAGCAT k-d10-kekek  79  649
    935634 4171 4186 22288 22303 TGCTTGAGGTTTTCCT k-d10-kekek  64  548
    935635 2914 2929 21031 21046 AGTATGAGAAACGGCC k-d10-kekek  90 1045
    935636 4199 4214 22316 22331 CTATAGTGTTCCAGGA k-d10-kekek  66  552
    935637 3069 3084 21186 21201 CTTGATAAAGGCTGAA k-d10-kekek  83 1427
    935638 3250 3265 21367 21382 ACTTTTAGAGAGGAGA k-d10-kekek  68 1960
    935639 4593 4608 22710 22725 CGGAAGTTTACACTGG k-d10-kekek  90 2119
    935640 N/A N/A  8466  8481 AAGCATTTTATCATCC k-d10-kekek  86 2628
    935641 N/A N/A 11117 11132 CAGTGATGTCAGGTTT k-d10-kekek  54 2629
    935642 5188 5203 23305 23320 CCTCAGTTTGTGAAGC k-d10-kekek  74 1894
    935643 4173 4188 22290 22305 ACTGCTTGAGGTTTTC k-d10-kekek  78 1356
    935644 2916 2931 21033 21048 GTAGTATGAGAAACGG k-d10-kekek  54 426
    935645 4201 4216 22318 22333 CTCTATAGTGTTCCAG k-d10-kekek  76 1811
    935646 3071 3086 21188 21203 AGCTTGATAAAGGCTG k-d10-kekek  99 1579
    935647 3252 3267 21369 21384 ACACTTTTAGAGAGGA k-d10-kekek 106 2111
    935648 4228 4243 22345 22360 AGTTGTAAATGAGTCG k-d10-kekek  56 2021
    935649 4594 4609 22711 22726 ACGGAAGTTTACACTG k-d10-kekek  93 2195
    935650 N/A N/A  8467  8482 GAAGCATTTTATCATC k-d10-kekek 112 2630
    935651 N/A N/A 11118 11133 GCAGTGATGTCAGGTT k-d10-kekek  64 2631
    935652 5189 5204 23306 23321 ACCTCAGTTTGTGAAG k-d10-kekek  82 1971
    935653 4174 4189 22291 22306 TACTGCTTGAGGTTTT k-d10-kekek  76 1433
    935654 2917 2932 21034 21049 TGTAGTATGAGAAACG k-d10-kekek  93 1197
    935655 4202 4217 22319 22334 TCTCTATAGTGTTCCA k-d10-kekek  39 2632
    935656 3072 3087 21189 21204 AAGCTTGATAAAGGCT k-d10-kekek  97 2633
    935657 3253 3268 21370 21385 GACACTTTTAGAGAGG k-d10-kekek  77  451
    935658 4229 4244 22346 22361 CAGTTGTAAATGAGTC k-d10-kekek  35  560
    935659 4592 4607 22709 22724 GGAAGTTTACACTGGA kk-d9-kekek  53 2044
    935660 N/A N/A  8465  8480 AGCATTTTATCATCCG kk-d9-kekek  61 1679
    935661 N/A N/A 11116 11131 AGTGATGTCAGGTTTT kk-d9-kekek  61 1232
    935662 5187 5202 23304 23319 CTCAGTTTGTGAAGCA kk-d9-kekek  78 1817
    935663 4172 4187 22289 22304 CTGCTTGAGGTTTTCC kk-d9-kekek  70 1279
    935664 2915 2930 21032 21047 TAGTATGAGAAACGGC kk-d9-kekek  73 1121
    935665 4200 4215 22317 22332 TCTATAGTGTTCCAGG kk-d9-kekek  72 1734
    935666 3070 3085 21187 21202 GCTTGATAAAGGCTGA kk-d9-kekek  93 1505
  • TABLE 39
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ SEQ SEQ SEQ
    ID: 1 ID: 1 ID: 2 ID: 2 IRF4 SEQ
    Compound Start Stop Start Stop (% ID
    Number Site Site Site Site Sequence Motif UTC) NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT kkk-d10-kkk  37  195
    881450 3252 3267 21369 21384 ACACTTTTAGAGAGGA kkk-d10-kkk  49 2111
    881659 4592 4607 22709 22724 GGAAGTTTACACTGGA kkk-d10-kkk  15 2044
    935667 3251 3266 21368 21383 CACTTTTAGAGAGGAG kk-d9-kekek  83 2036
    935668 4591 4606 22708 22723 GAAGTTTACACTGGAT kk-d9-kekek  45 1968
    935669 N/A N/A  8464  8479 GCATTTTATCATCCGA kk-d9-kekek  52 1605
    935670 N/A N/A 11115 11130 GTGATGTCAGGTTTTC kk-d9-kekek  60 2627
    935671 5186 5201 23303 23318 TCAGTTTGTGAAGCAT kk-d9-kekek  42  649
    935672 4171 4186 22288 22303 TGCTTGAGGTTTTCCT kk-d9-kekek  64  548
    935673 2914 2929 21031 21046 AGTATGAGAAACGGCC kk-d9-kekek  97 1045
    935674 4199 4214 22316 22331 CTATAGTGTTCCAGGA kk-d9-kekek  57  552
    935675 3069 3084 21186 21201 CTTGATAAAGGCTGAA kk-d9-kekek  88 1427
    935676 3250 3265 21367 21382 ACTTTTAGAGAGGAGA kk-d9-kekek  60 1960
    935677 4593 4608 22710 22725 CGGAAGTTTACACTGG kk-d9-kekek  80 2119
    935678 N/A N/A  8466  8481 AAGCATTTTATCATCC kk-d9-kekek  82 2628
    935679 N/A N/A 11117 11132 CAGTGATGTCAGGTTT kk-d9-kekek  36 2629
    935680 5188 5203 23305 23320 CCTCAGTTTGTGAAGC kk-d9-kekek  85 1894
    935681 4173 4188 22290 22305 ACTGCTTGAGGTTTTC kk-d9-kekek  76 1356
    935682 2916 2931 21033 21048 GTAGTATGAGAAACGG kk-d9-kekek  50  426
    935683 4201 4216 22318 22333 CTCTATAGTGTTCCAG kk-d9-kekek  78 1811
    935684 3071 3086 21188 21203 AGCTTGATAAAGGCTG kk-d9-kekek  84 1579
    935685 3252 3267 21369 21384 ACACTTTTAGAGAGGA kk-d9-kekek  73 2111
    935686 4228 4243 22345 22360 AGTTGTAAATGAGTCG kk-d9-kekek  44 2021
    935687 4594 4609 22711 22726 ACGGAAGTTTACACTG kk-d9-kekek  79 2195
    935688 N/A N/A  8467  8482 GAAGCATTTTATCATC kk-d9-kekek 120 2630
    935689 N/A N/A 11118 11133 GCAGTGATGTCAGGTT kk-d9-kekek  31 2631
    935690 5189 5204 23306 23321 ACCTCAGTTTGTGAAG kk-d9-kekek  87 1971
    935691 4174 4189 22291 22306 TACTGCTTGAGGTTTT kk-d9-kekek  78 1433
    935692 2917 2932 21034 21049 TGTAGTATGAGAAACG kk-d9-kekek  88 1197
    935693 4202 4217 22319 22334 TCTCTATAGTGTTCCA kk-d9-kekek  72 2632
    935694 3072 3087 21189 21204 AAGCTTGATAAAGGCT kk-d9-kekek 119 2633
    935695 3253 3268 21370 21385 GACACTTTTAGAGAGG kk-d9-kekek  83  451
    935696 4229 4244 22346 22361 CAGTTGTAAATGAGTC kk-d9-kekek  19  560
    935697 4592 4607 22709 22724 GGAAGTTTACACTGGA kkk-d9-kkke  22 2044
    935698 N/A N/A  8465  8480 AGCATTTTATCATCCG kkk-d9-kkke  34 1679
    935699 N/A N/A 11116 11131 AGTGATGTCAGGTTTT kkk-d9-kkke  35 1232
    935700 5187 5202 23304 23319 CTCAGTTTGTGAAGCA kkk-d9-kkke  31 1817
    935701 4172 4187 22289 22304 CTGCTTGAGGTTTTCC kkk-d9-kkke  35 1279
    935702 2915 2930 21032 21047 TAGTATGAGAAACGGC kkk-d9-kkke  52 1121
    935703 4200 4215 22317 22332 TCTATAGTGTTCCAGG kkk-d9-kkke  48 1734
    935704 3070 3085 21187 21202 GCTTGATAAAGGCTGA kkk-d9-kkke  77 1505
    935705 3251 3266 21368 21383 CACTTTTAGAGAGGAG kkk-d9-kkke  60 2036
    935706 4591 4606 22708 22723 GAAGTTTACACTGGAT kkk-d9-kkke  55 1968
    935707 N/A N/A  8464  8479 GCATTTTATCATCCGA kkk-d9-kkke  38 1605
    935708 N/A N/A 11115 11130 GTGATGTCAGGTTTTC kkk-d9-kkke  29 2627
    935709 5186 5201 23303 23318 TCAGTTTGTGAAGCAT kkk-d9-kkke  42  649
    935710 4171 4186 22288 22303 TGCTTGAGGTTTTCCT kkk-d9-kkke  54  548
    935711 2914 2929 21031 21046 AGTATGAGAAACGGCC kkk-d9-kkke  93 1045
    935712 4199 4214 22316 22331 CTATAGTGTTCCAGGA kkk-d9-kkke  69  552
    935713 3069 3084 21186 21201 CTTGATAAAGGCTGAA kkk-d9-kkke  64 1427
    935714 3250 3265 21367 21382 ACTTTTAGAGAGGAGA kkk-d9-kkke  64 1960
    935715 4593 4608 22710 22725 CGGAAGTTTACACTGG kkk-d9-kkke  75 2119
    935716 N/A N/A  8466  8481 AAGCATTTTATCATCC kkk-d9-kkke  67 2628
    935717 N/A N/A 11117 11132 CAGTGATGTCAGGTTT kkk-d9-kkke  51 2629
    935718 5188 5203 23305 23320 CCTCAGTTTGTGAAGC kkk-d9-kkke  98 1894
    935719 4173 4188 22290 22305 ACTGCTTGAGGTTTTC kkk-d9-kkke  48 1356
    935720 2916 2931 21033 21048 GTAGTATGAGAAACGG kkk-d9-kkke  60  426
    935721 4201 4216 22318 22333 CTCTATAGTGTTCCAG kkk-d9-kkke  35 1811
    935722 3071 3086 21188 21203 AGCTTGATAAAGGCTG kkk-d9-kkke  98 1579
    935723 3252 3267 21369 21384 ACACTTTTAGAGAGGA kkk-d9-kkke  71 2111
    935724 4228 4243 22345 22360 AGTTGTAAATGAGTCG kkk-d9-kkke  13 2021
    935725 4594 4609 22711 22726 ACGGAAGTTTACACTG kkk-d9-kkke  71 2195
    935726 N/A N/A  8467  8482 GAAGCATTTTATCATC kkk-d9-kkke  99 2630
    935727 N/A N/A 11118 11133 GCAGTGATGTCAGGTT kkk-d9-kkke  38 2631
    935728 5189 5204 23306 23321 ACCTCAGTTTGTGAAG kkk-d9-kkke  90 1971
    935729 4174 4189 22291 22306 TACTGCTTGAGGTTTT kkk-d9-kkke  87 1433
    935730 2917 2932 21034 21049 TGTAGTATGAGAAACG kkk-d9-kkke  67 1197
    935731 4202 4217 22319 22334 TCTCTATAGTGTTCCA kkk-d9-kkke  44 2632
    935732 3072 3087 21189 21204 AAGCTTGATAAAGGCT kkk-d9-kkke  95 2633
    935733 3253 3268 21370 21385 GACACTTTTAGAGAGG kkk-d9-kkke  76  451
    935734 4229 4244 22346 22361 CAGTTGTAAATGAGTC kkk-d9-kkke  32  560
    935735 4592 4607 22709 22724 GGAAGTTTACACTGGA kk-d10-keke  54 2044
    935736 N/A N/A  8465  8480 AGCATTTTATCATCCG kk-d10-keke  67 1679
    935737 N/A N/A 11116 11131 AGTGATGTCAGGTTTT kk-d10-keke  68 1232
    935738 5187 5202 23304 23319 CTCAGTTTGTGAAGCA kk-d10-keke  70 1817
    935739 4172 4187 22289 22304 CTGCTTGAGGTTTTCC kk-d10-keke  56 1279
    935740 2915 2930 21032 21047 TAGTATGAGAAACGGC kk-d10-keke  54 1121
    935741 4200 4215 22317 22332 TCTATAGTGTTCCAGG kk-d10-keke  34 1734
    935742 3070 3085 21187 21202 GCTTGATAAAGGCTGA kk-d10-keke  69 1505
  • TABLE 40
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID: SEQ ID: SEQ ID: IRF4 SEQ
    Compound 1 Start 1 Stop 2 Start 2 Stop (% ID
    Number Site Site Site Site Sequence Motif UTC) NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT kkk-d10-kkk  37  195
    881450 3252 3267 21369 21384 ACACTTTTAGAGAGGA kkk-d10-kkk  53 2111
    881659 4592 4607 22709 22724 GGAAGTTTACACTGGA kkk-d10-kkk  20 2044
    935743 3251 3266 21368 21383 CACTTTTAGAGAGGAG kk-d10-keke  73 2036
    935744 4591 4606 22708 22723 GAAGTTTACACTGGAT kk-d10-keke  54 1968
    935745 N/A N/A  8464  8479 GCATTTTATCATCCGA kk-d10-keke  61 1605
    935746 N/A N/A 11115 11130 GTGATGTCAGGTTTTC kk-d10-keke  82 2627
    935747 5186 5201 23303 23318 TCAGTTTGTGAAGCAT kk-d10-keke  67  649
    935748 4171 4186 22288 22303 TGCTTGAGGTTTTCCT kk-d10-keke  67  548
    935749 2914 2929 21031 21046 AGTATGAGAAACGGCC kk-d10-keke  91 1045
    935750 4199 4214 22316 22331 CTATAGTGTTCCAGGA kk-d10-keke  64  552
    935751 3069 3084 21186 21201 CTTGATAAAGGCTGAA kk-d10-keke  96 1427
    935752 3250 3265 21367 21382 ACTTTTAGAGAGGAGA kk-d10-keke  77 1960
    935753 4593 4608 22710 22725 CGGAAGTTTACACTGG kk-d10-keke  67 2119
    935754 N/A N/A  8466  8481 AAGCATTTTATCATCC kk-d10-keke  80 2628
    935755 N/A N/A 11117 11132 CAGTGATGTCAGGTTT kk-d10-keke  59 2629
    935756 5188 5203 23305 23320 CCTCAGTTTGTGAAGC kk-d10-keke  84 1894
    935757 4173 4188 22290 22305 ACTGCTTGAGGTTTTC kk-d10-keke  79 1356
    935758 2916 2931 21033 21048 GTAGTATGAGAAACGG kk-d10-keke  72  426
    935759 4201 4216 22318 22333 CTCTATAGTGTTCCAG kk-d10-keke  73 1811
    935760 3071 3086 21188 21203 AGCTTGATAAAGGCTG kk-d10-keke  99 1579
    935761 3252 3267 21369 21384 ACACTTTTAGAGAGGA kk-d10-keke  86 2111
    935762 4228 4243 22345 22360 AGTTGTAAATGAGTCG kk-d10-keke  41 2021
    935763 4594 4609 22711 22726 ACGGAAGTTTACACTG kk-d10-keke  87 2195
    935764 N/A N/A  8467  8482 GAAGCATTTTATCATC kk-d10-keke 107 2630
    935765 N/A N/A 11118 11133 GCAGTGATGTCAGGTT kk-d10-keke  33 2631
    935766 5189 5204 23306 23321 ACCTCAGTTTGTGAAG kk-d10-keke 112 1971
    935767 4174 4189 22291 22306 TACTGCTTGAGGTTTT kk-d10-keke  89 1433
    935768 2917 2932 21034 21049 TGTAGTATGAGAAACG kk-d10-keke  90 1197
    935769 4202 4217 22319 22334 TCTCTATAGTGTTCCA kk-d10-keke  73 2632
    935770 3072 3087 21189 21204 AAGCTTGATAAAGGCT kk-d10-keke 118 2633
    935771 3253 3268 21370 21385 GACACTTTTAGAGAGG kk-d10-keke  91  451
    935772 4229 4244 22346 22361 CAGTTGTAAATGAGTC kk-d10-keke  41  560
    935773 4592 4607 22709 22724 GGAAGTTTACACTGGA kk-d9-kdkdk  76 2044
    935774 N/A N/A  8465  8480 AGCATTTTATCATCCG kk-d9-kdkdk  89 1679
    935775 N/A N/A 11116 11131 ATGATGTCAGGTTTT kk-d9-kdkdk  69 1232
    935776 5187 5202 23304 23319 CTCAGTTTGTGAAGCA kk-d9-kdkdk 101 1817
    935777 4172 4187 22289 22304 CTGCTTGAGGTTTTCC kk-d9-kdkdk  64 1279
    935778 2915 2930 21032 21047 TAGTATGAGAAACGGC kk-d9-kdkdk  61 1121
    935779 4200 4215 22317 22332 TCTATAGTGTTCCAGG kk-d9-kdkdk  50 1734
    935780 3070 3085 21187 21202 GCTTGATAAAGGCTGA kk-d9-kdkdk  96 1505
    935781 3251 3266 21368 21383 CACTTTTAGAGAGGAG kk-d9-kdkdk  84 2036
    935782 4227 4242 22344 22359 GTTGTAAATGAGTCGG kk-d9-kdkdk  42  559
    935783 4591 4606 22708 22723 GAAGTTTACACTGGAT kk-d9-kdkdk  77 1968
    935784 N/A N/A  8464  8479 GCATTTTATCATCCGA kk-d9-kdkdk  84 1605
    935785 N/A N/A 11115 11130 GTGATGTCAGGTTTTC kk-d9-kdkdk  73 2627
    935786 5186 5201 23303 23318 TCAGTTTGTGAAGCAT kk-d9-kdkdk  75  649
    935787 4171 4186 22288 22303 TGCTTGAGGTTTTCCT kk-d9-kdkdk  55  548
    935788 2914 2929 21031 21046 AGTATGAGAAACGGCC kk-d9-kdkdk  94 1045
    935789 4199 4214 22316 22331 CTATAGTGTTCCAGGA kk-d9-kdkdk  51  552
    935790 3069 3084 21186 21201 CTTGATAAAGGCTGAA kk-d9-kdkdk  99 1427
    935791 3250 3265 21367 21382 ACTTTTAGAGAGGAGA kk-d9-kdkdk  66 1960
    935792 4226 4241 22343 22358 TTGTAAATGAGTCGGT kk-d9-kdkdk  57  195
    935793 4593 4608 22710 22725 CGGAAGTTTACACTGG kk-d9-kdkdk  87 2119
    935794 N/A N/A  8466  8481 AAGCATTTTATCATCC kk-d9-kdkdk  97 2628
    935795 N/A N/A 11117 11132 CAGTGATGTCAGGTTT kk-d9-kdkdk  53 2629
    935796 5188 5203 23305 23320 CCTCAGTTTGTGAAGC kk-d9-kdkdk  92 1894
    935797 4173 4188 22290 22305 ACTGCTTGAGGTTTTC kk-d9-kdkdk  81 1356
    935798 2916 2931 21033 21048 GTAGTATGAGAAACGG kk-d9-kdkdk  68  426
    935799 4201 4216 22318 22333 CTCTATAGTGTTCCAG kk-d9-kdkdk  69 1811
    935800 3071 3086 21188 21203 AGCTTGATAAAGGCTG kk-d9-kdkdk 103 1579
    935801 3252 3267 21369 21384 ACACTTTTAGAGAGGA kk-d9-kdkdk  97 2111
    935802 4228 4243 22345 22360 AGTTGTAAATGAGTCG kk-d9-kdkdk  61 2021
    935803 4594 4609 22711 22726 ACGGAAGTTTACACTG kk-d9-kdkdk 102 2195
    935804 N/A N/A  8467  8482 GAAGCATTTTATCATC kk-d9-kdkdk  99 2630
    935805 N/A N/A 11118 11133 GCAGTGATGTCAGGTT kk-d9-kdkdk  47 2631
    935806 5189 5204 23306 23321 ACCTCAGTTTGTGAAG kk-d9-kdkdk 103 1971
    935807 4174 4189 22291 22306 TACTGCTTGAGGTTTT kk-d9-kdkdk  85 1433
    935808 2917 2932 21034 21049 TGTAGTATGAGAAACG kk-d9-kdkdk 106 1197
    935809 4202 4217 22319 22334 TCTCTATAGTGTTCCA kk-d9-kdkdk  62 2632
    935810 3072 3087 21189 21204 AAGCTTGATAAAGGCT kk-d9-kdkdk 102 2633
    935811 3253 3268 21370 21385 GACACTTTTAGAGAGG kk-d9-kdkdk  86  451
    935812 4229 4244 22346 22361 CAGTTGTAAATGAGTC kk-d9-kdkdk  54  560
    935813 4592 4607 22709 22724 GGAAGTTTACACTGGA kkk-d8-  57 2044
    kekek
    935814 N/A N/A  8465  8480 AGCATTTTATCATCCG kkk-d8-  78 1679
    kekek
    935815 N/A N/A 11116 11131 AGTGATGTCAGGTTTT kkk-d8-  63 1232
    kekek
    935816 5187 5202 23304 23319 CTCAGTTTGTGAAGCA kkk-d8-  63 1817
    kekek
    935817 4172 4187 22289 22304 CTGCTTGAGGTTTTCC kkk-d8-  74 1279
    kekek
    935818 2915 2930 21032 21047 TAGTATGAGAAACGGC kkk-d8-  70 1121
    kekek
  • TABLE 41
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID: SEQ ID: SEQ ID: IRF4 SEQ
    Compound 1 Start 1 Stop 2 Start 2 Stop (% ID
    Number Site Site Site Site Sequence Motif UTC) NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT kkk-d10-kkk  34  195
    881450 3252 3267 21369 21384 ACACTTTTAGAGAGGA kkk-d10-kkk  63 2111
    881659 4592 4607 22709 22724 GGAAGTTTACACTGGA kkk-d10-kkk  17 2044
    935819 4200 4215 22317 22332 TCTATAGTGTTCCAGG kkk-d8-  87 1734
    kekek
    935820 3070 3085 21187 21202 GCTTGATAAAGGCTGA kkk-d8-  99 1505
    kekek
    935821 3251 3266 21368 21383 CACTTTTAGAGAGGAG kkk-d8-  93 2036
    kekek
    935822 4591 4606 22708 22723 GAAGTTTACACTGGAT kkk-d8-  48 1968
    kekek
    935823 N/A N/A  8464  8479 GCATTTTATCATCCGA kkk-d8-  55 1605
    kekek
    935824 N/A N/A 11115 11130 GTGATGTCAGGTTTTC kkk-d8-  43 2627
    kekek
    935825 5186 5201 23303 23318 TCAGTTTGTGAAGCAT kkk-d8-  59  649
    kekek
    935826 4171 4186 22288 22303 TGCTTGAGGTTTTCCT kkk-d8-  73  548
    kekek
    935827 2914 2929 21031 21046 AGTATGAGAAACGGCC kkk-d8-  90 1045
    kekek
    935828 4199 4214 22316 22331 CTATAGTGTTCCAGGA kkk-d8-  77  552
    kekek
    935829 3069 3084 21186 21201 CTTGATAAAGGCTGAA kkk-d8-  88 1427
    kekek
    935830 3250 3265 21367 21382 ACTTTTAGAGAGGAGA kkk-d8-  79 1960
    kekek
    935831 4593 4608 22710 22725 CGGAAGTTTACACTGG kkk-d8-  82 2119
    kekek
    935832 N/A N/A  8466  8481 AAGCATTTTATCATCC kkk-d8-  90 2628
    kekek
    935833 N/A N/A 11117 11132 CAGTGATGTCAGGTTT kkk-d8-  44 2629
    kekek
    935834 5188 5203 23305 23320 CCTCAGTTTGTGAAGC kkk-d8-  97 1894
    kekek
    935835 4173 4188 22290 22305 ACTGCTTGAGGTTTTC kkk-d8-  68 1356
    kekek
    935836 2916 2931 21033 21048 GTAGTATGAGAAACGG kkk-d8-  57  426
    kekek
    935837 4201 4216 22318 22333 CTCTATAGTGTTCCAG kkk-d8-  85 1811
    kekek
    935838 3071 3086 21188 21203 AGCTTGATAAAGGCTG kkk-d8- 108 1579
    kekek
    935839 3252 3267 21369 21384 ACACTTTTAGAGAGGA kkk-d8-  85 2111
    kekek
    935840 4228 4243 22345 22360 AGTTGTAAATGAGTCG kkk-d8-  39 2021
    kekek
    935841 4594 4609 22711 22726 ACGGAAGTTTACACTG kkk-d8-  86 2195
    kekek
    935842 N/A N/A  8467  8482 GAAGCATTTTATCATC kkk-d8- 105 2630
    kekek
    935843 N/A N/A 11118 11133 GCAGTGATGTCAGGTT kkk-d8-  64 2631
    kekek
    935844 5189 5204 23306 23321 ACCTCAGTTTGTGAAG kkk-d8- 103 1971
    kekek
    935845 4174 4189 22291 22306 TACTGCTTGAGGTTTT kkk-d8- 108 1433
    kekek
    935846 2917 2932 21034 21049 TGTAGTATGAGAAACG kkk-d8-  77 1197
    kekek
    935847 4202 4217 22319 22334 TCTCTATAGTGTTCCA kkk-d8-  92 2632
    kekek
    935848 3072 3087 21189 21204 AAGCTTGATAAAGGCT kkk-d8- 104 2633
    kekek
    935849 3253 3268 21370 21385 GACACTTTTAGAGAGG kkk-d8- 108  451
    kekek
    935850 4229 4244 22346 22361 CAGTTGTAAATGAGTC kkk-d8-  24  560
    kekek
    935851 4592 4607 22709 22724 GGAAGTTTACACTGGA kkk-d9-keke  22 2044
    935852 N/A N/A  8465  8480 AGCATTTTATCATCCG kkk-d9-keke  58 1679
    935853 N/A N/A 11116 11131 AGTGATGTCAGGTTTT kkk-d9-keke  41 1232
    935854 5187 5202 23304 23319 CTCAGTTTGTGAAGCA kkk-d9-keke  36 1817
    935855 4172 4187 22289 22304 CTGCTTGAGGTTTTCC kkk-d9-keke  50 1279
    935856 2915 2930 21032 21047 TAGTATGAGAAACGGC kkk-d9-keke  38 1121
    935857 4200 4215 22317 22332 TCTATAGTGTTCCAGG kkk-d9-keke  32 1734
    935858 3070 3085 21187 21202 GCTTGATAAAGGCTGA kkk-d9-keke  76 1505
    935859 3251 3266 21368 21383 CACTTTTAGAGAGGAG kkk-d9-keke  43 2036
    935860 4591 4606 22708 22723 GAAGTTTACACTGGAT kkk-d9-keke  51 1968
    935861 N/A N/A  8464  8479 GCATTTTATCATCCGA kkk-d9-keke  68 1605
    935862 N/A N/A 11115 11130 GTGATGTCAGGTTTTC kkk-d9-keke  66 2627
    935863 5186 5201 23303 23318 TCAGTTTGTGAAGCAT kkk-d9-keke  47  649
    935864 4171 4186 22288 22303 TGCTTGAGGTTTTCCT kkk-d9-keke  65  548
    935865 2914 2929 21031 21046 AGTATGAGAAACGGCC kkk-d9-keke  84 1045
    935866 4199 4214 22316 22331 CTATAGTGTTCCAGGA kkk-d9-keke  78  552
    935867 3069 3084 21186 21201 CTTGATAAAGGCTGAA kkk-d9-keke  76 1427
    935868 3250 3265 21367 21382 ACTTTTAGAGAGGAGA kkk-d9-keke  59 1960
    935869 4593 4608 22710 22725 CGGAAGTTTACACTGG kkk-d9-keke  58 2119
    935870 N/A N/A  8466  8481 AAGCATTTTATCATCC kkk-d9-keke  79 2628
    935871 N/A N/A 11117 11132 CAGTGATGTCAGGTTT kkk-d9-keke  66 2629
    935872 5188 5203 23305 23320 CCTCAGTTTGTGAAGC kkk-d9-keke  92 1894
    935873 4173 4188 22290 22305 ACTGCTTGAGGTTTTC kkk-d9-keke  62 1356
    935874 2916 2931 21033 21048 GTAGTATGAGAAACGG kkk-d9-keke  85  426
    935875 4201 4216 22318 22333 CTCTATAGTGTTCCAG kkk-d9-keke  51 1811
    935876 3071 3086 21188 21203 AGCTTGATAAAGGCTG kkk-d9-keke 108 1579
    935877 3252 3267 21369 21384 ACACTTTTAGAGAGGA kkk-d9-keke  63 2111
    935878 4228 4243 22345 22360 AGTTGTAAATGAGTCG kkk-d9-keke  23 2021
    935879 4594 4609 22711 22726 ACGGAAGTTTACACTG kkk-d9-keke  87 2195
    935880 N/A N/A  8467  8482 GAAGCATTTTATCATC kkk-d9-keke  92 2630
    935881 N/A N/A 11118 11133 GCAGTGATGTCAGGTT kkk-d9-keke  44 2631
    935882 5189 5204 23306 23321 ACCTCAGTTTGTGAAG kkk-d9-keke  92 1971
    935883 4174 4189 22291 22306 TACTGCTTGAGGTTTT kkk-d9-keke  93 1433
    935884 2917 2932 21034 21049 TGTAGTATGAGAAACG kkk-d9-keke  71 1197
    935885 4202 4217 22319 22334 TCTCTATAGTGTTCCA kkk-d9-keke  67 2632
    935886 3072 3087 21189 21204 AAGCTTGATAAAGGCT kkk-d9-keke 118 2633
    935887 3253 3268 21370 21385 GACACTTTTAGAGAGG kkk-d9-keke  76  451
    935888 4229 4244 22346 22361 CAGTTGTAAATGAGTC kkk-d9-keke  42  560
    935889 4592 4607 22709 22724 GGAAGTTTACACTGGA kk-d9-eeekk  53 2044
    935890 N/A N/A  8465  8480 AGCATTTTATCATCCG kk-d9-eeekk  72 1679
    935891 N/A N/A 11116 11131 AGTGATGTCAGGTTTT kk-d9-eeekk  75 1232
    935892 5187 5202 23304 23319 CTCAGTTTGTGAAGCA kk-d9-eeekk  82 1817
    935893 4172 4187 22289 22304 CTGCTTGAGGTTTTCC kk-d9-eeekk  69 1279
    935894 2915 2930 21032 21047 TAGTATGAGAAACGGC kk-d9-eeekk  63 1121
  • TABLE 42
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID: SEQ ID: SEQ ID: IRF4 SEQ
    Compound 1 Start 1 Stop 2 Start 2 Stop (% ID
    Number Site Site Site Site Sequence Motif UTC) NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT kkk-d10-kkk  31  195
    881450 3252 3267 21369 21384 ACACTTTTAGAGAGGA kkk-d10-kkk  54 2111
    881659 4592 4607 22709 22724 GGAAGTTTACACTGGA kkk-d10-kkk  15 2044
    935971 N/A N/A 11116 11131 AGTGATGTCAGGTTTT k-d9-kekeke  60 1232
    935972 5187 5202 23304 23319 CTCAGTTTGTGAAGCA k-d9-kekeke  81 1817
    935973 4172 4187 22289 22304 CTGCTTGAGGTTTTCC k-d9-kekeke  80 1279
    935974 2915 2930 21032 21047 TAGTATGAGAAACGGC k-d9-kekeke  68 1121
    935975 4200 4215 22317 22332 TCTATAGTGTTCCAGG k-d9-kekeke  88 1734
    935976 3070 3085 21187 21202 GCTTGATAAAGGCTGA k-d9-kekeke 101 1505
    935977 3251 3266 21368 21383 CACTTTTAGAGAGGAG k-d9-kekeke  91 2036
    935978 4591 4606 22708 22723 GAAGTTTACACTGGAT k-d9-kekeke  89 1968
    935979 N/A N/A  8464  8479 GCATTTTATCATCCGA k-d9-kekeke  77 1605
    935980 N/A N/A 11115 11130 GTGATGTCAGGTTTTC k-d9-kekeke  70 2627
    935981 5186 5201 23303 23318 TCAGTTTGTGAAGCAT k-d9-kekeke  91  649
    935982 4171 4186 22288 22303 TGCTTGAGGTTTTCCT k-d9-kekeke  91  548
    935983 2914 2929 21031 21046 AGTATGAGAAACGGCC k-d9-kekeke  96 1045
    935984 4199 4214 22316 22331 CTATAGTGTTCCAGGA k-d9-kekeke  88  552
    935985 3069 3084 21186 21201 CTTGATAAAGGCTGAA k-d9-kekeke  95 1427
    935986 3250 3265 21367 21382 ACTTTTAGAGAGGAGA k-d9-kekeke  83 1960
    935987 4593 4608 22710 22725 CGGAAGTTTACACTGG k-d9-kekeke  83 2119
    935988 N/A N/A  8466  8481 AAGCATTTTATCATCC k-d9-kekeke  94 2628
    935989 N/A N/A 11117 11132 CAGTGATGTCAGGTTT k-d9-kekeke  52 2629
    935990 5188 5203 23305 23320 CCTCAGTTTGTGAAGC k-d9-kekeke  89 1894
    935991 4173 4188 22290 22305 ACTGCTTGAGGTTTTC k-d9-kekeke  79 1356
    935992 2916 2931 21033 21048 GTAGTATGAGAAACGG k-d9-kekeke  72  426
    935993 4201 4216 22318 22333 CTCTATAGTGTTCCAG k-d9-kekeke  89 1811
    935994 3071 3086 21188 21203 AGCTTGATAAAGGCTG k-d9-kekeke  98 1579
    935995 3252 3267 21369 21384 ACACTTTTAGAGAGGA k-d9-kekeke  94 2111
    935996 4228 4243 22345 22360 AGTTGTAAATGAGTCG k-d9-kekeke  53 2021
    935997 4594 4609 22711 22726 ACGGAAGTTTACACTG k-d9-kekeke  98 2195
    935998 N/A N/A  8467  8482 GAAGCATTTTATCATC k-d9-kekeke  96 2630
    935999 N/A N/A 11118 11133 GCAGTGATGTCAGGTT k-d9-kekeke  67 2631
    936000 5189 5204 23306 23321 ACCTCAGTTTGTGAAG k-d9-kekeke  84 1971
    936001 4174 4189 22291 22306 TACTGCTTGAGGTTTT k-d9-kekeke  86 1433
    936002 2917 2932 21034 21049 TGTAGTATGAGAAACG k-d9-kekeke  86 1197
    936003 4202 4217 22319 22334 TCTCTATAGTGTTCCA k-d9-kekeke  82 2632
    936004 3072 3087 21189 21204 AAGCTTGATAAAGGCT k-d9-kekeke  98 2633
    936005 3253 3268 21370 21385 GACACTTTTAGAGAGG k-d9-kekeke  91  451
    936006 4229 4244 22346 22361 CAGTTGTAAATGAGTC k-d9-kekeke  38  560
    936007 4592 4607 22709 22724 GGAAGTTTACACTGGA ekk-d9-kkce  45 2044
    936008 N/A N/A  8465  8480 AGCATTTTATCATCCG ekk-d9-kkce  57 1679
    936009 N/A N/A 11116 11131 AGTGATGTCAGGTTTT ekk-d9-kkee  61 1232
    936010 5187 5202 23304 23319 CTCAGTTTGTGAAGCA ekk-d9-kkee  55 1817
    936011 4172 4187 22289 22304 CTGCTTGAGGTTTTCC ekk-d9-kkee  48 1279
    936012 2915 2930 21032 21047 TAGTATGAGAAACGGC ekk-d9-kkee  62 1121
    936013 4200 4215 22317 22332 TCTATAGTGTTCCAGG ekk-d9-kkee  42 1734
    936014 3070 3085 21187 21202 GCTTGATAAAGGCTGA ekk-d9-kkee  65 1505
    936015 3251 3266 21368 21383 CACTTTTAGAGAGGAG ekk-d9-kkee  59 2036
    936016 4227 4242 22344 22359 GTTGTAAATGAGTCGG ekk-d9-kkee  31  559
    936017 4591 4606 22708 22723 GAAGTTTACACTGGAT ekk-d9-kkee  52 1968
    936018 N/A N/A  8464  8479 GCATTTTATCATCCGA ekk-d9-kkee  39 1605
    936019 N/A N/A 11115 11130 GTGATGTCAGGTTTTC ekk-d9-kkee  52 2627
    936020 5186 5201 23303 23318 TCAGTTTGTGAAGCAT ekk-d9-kkee  53  649
    936021 4171 4186 22288 22303 TGCTTGAGGTTTTCCT ekk-d9-kkee  65  548
    936022 2914 2929 21031 21046 AGTATGAGAAACGGCC ekk-d9-kkee  88 1045
    936023 4199 4214 22316 22331 CTATAGTGTTCCAGGA ekk-d9-kkee  92  552
    936024 3069 3084 21186 21201 CTTGATAAAGGCTGAA ekk-d9-kkee  83 1427
    936025 3250 3265 21367 21382 ACTTTTAGAGAGGAGA ekk-d9-kkee  72 1960
    936026 4226 4241 22343 22358 TTGTAAATGAGTCGGT ekk-d9-kkee  49  195
    936027 4593 4608 22710 22725 CGGAAGTTTACACTGG ekk-d9-kkee  76 2119
    936028 N/A N/A  8466  8481 AAGCATTTTATCATCC ekk-d9-kkee  86 2628
    936029 N/A N/A 11117 11132 CAGTGATGTCAGGTTT ekk-d9-kkee  80 2629
    936030 5188 5203 23305 23320 CCTCAGTTTGTGAAGC ekk-d9-kkee  89 1894
    936031 4173 4188 22290 22305 ACTGCTTGAGGTTTTC ekk-d9-kkee  54 1356
    936032 2916 2931 21033 21048 GTAGTATGAGAAACGG ekk-d9-kkee  71  426
    936033 4201 4216 22318 22333 CTCTATAGTGTTCCAG ekk-d9-kkee  41 1811
    936034 3071 3086 21188 21203 AGCTTGATAAAGGCTG ekk-d9-kkee  99 1579
    936035 3252 3267 21369 21384 ACACTTTTAGAGAGGA ekk-d9-kkee  71 2111
    936036 4228 4243 22345 22360 AGTTGTAAATGAGTCG ekk-d9-kkee  51 2021
    936037 4594 4609 22711 22726 ACGGAAGTTTACACTG ekk-d9-kkee  83 2195
    936038 N/A N/A  8467  8482 GAAGCATTTTATCATC ekk-d9-kkee  99 2630
    936039 N/A N/A 11118 11133 GCAGTGATGTCAGGTT ekk-d9-kkee  44 2631
    936040 5189 5204 23306 23321 ACCTCAGTTTGTGAAG ekk-d9-kkee  98 1971
    936041 4174 4189 22291 22306 TACTGCTTGAGGTTTT ekk-d9-kkee  94 1433
    936042 2917 2932 21034 21049 TGTAGTATGAGAAACG ekk-d9-kkee  94 1197
    936043 4202 4217 22319 22334 TCTCTATAGTGTTCCA ekk-d9-kkee  61 2632
    936044 3072 3087 21189 21204 AAGCTTGATAAAGGCT ekk-d9-kkee 101 2633
    936045 3253 3268 21370 21385 GACACTTTTAGAGAGG ekk-d9-kkee  76  451
    936046 4229 4244 22346 22361 CAGTTGTAAATGAGTC ekk-d9-kkee  45  560
  • Example 9: Effect of 3-10-3 cEt Gapmers with Phosphorothioate Internucleoside Linkages on Human IRF4 In Vitro, Single Dose
  • Modified oligonucleotides complementary to a human IRF4 nucleic acid were designed and tested for their effect on IRF4 mRNA in vitro.
  • Cultured MM.1R cells at a density of 5,000 cells per well were transfected by free uptake with 1,000 nM concentration of modified oligonucleotide or no modified oligonucleotide for untreated controls. After approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by quantitative real-time PCR. Human primer probe set hIRF4_LTS34726 (described hereinabove in Example 7) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN®. Results are presented in the table below as percent control of the amount of IRF4 mRNA, relative to untreated control (UTC) cells.
  • The modified oligonucleotides in Tables 43 through 52 are 3-10-3 cEt gapmers. The gapmers are 16 nucleobases in length, wherein the central gap segment comprises ten 2′-deoxynucleosides and is flanked by wing segments on both the 5′ end and on the 3′ end comprising three cEt nucleosides. The sugar motif for the gapmers is (from 5′ to 3′): kkkddddddddddkkk; wherein represents a 2′-deoxyribose sugar and ‘k’ represents a cEt modified sugar. Each internucleoside linkage is a phosphorothioate internucleoside linkage and each cytosine residue is a 5-methylcytosine. “Start Site” indicates the 5′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence. “Stop Site” indicates the 3′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Each modified oligonucleotide listed in Tables 43 through 52 below is complementary to human IRF4 nucleic acid sequences SEQ ID NO: 1 or SEQ ID NO: 2, as indicated. ‘N/A’ indicates that the modified oligonucleotide is not complementary to that particular nucleic acid sequence with 100% complementarity. As shown below, modified oligonucleotides complementary to human IRF4 reduced the amount of human IRF4 mRNA.
  • TABLE 43
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID: SEQ ID: SEQ ID: IRF4 SEQ
    Compound 1 Start 1 Stop 2 Start 2 Stop (% ID
    Number Site Site Site Site Sequence UTC) NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT  37  195
    969844 N/A N/A  3801  3816 CCTTACCTCGCCCTGG 131 2657
    969854 N/A N/A  4265  4280 CGCCAGCGGGTGAGCA  81 2658
    969864 N/A N/A  4371  4386 GGCGACGACAGCTGCG 115 2659
    969874 N/A N/A  4518  4533 AGCTAGCGCGCACTAA 108 2660
    969884 N/A N/A  4836  4851 TCCTGTAACGCACCCG 113 2661
    969894 N/A N/A  5487  5502 CCTGATGCCTCCGCCG  94 2662
    969904 N/A N/A  5667  5682 CGAGAACGCACGGACG 111 2663
    969914 N/A N/A  5761  5776 GCACAGGCGCGGACGC 106 2664
    969924 N/A N/A  6002  6017 GTGCACTCGCGCAAAG 105 2665
    969934 N/A N/A  6266  6281 TGCGGAGGTTCCTTGA  88 2666
    969944 N/A N/A  6317  6332 CTGCCAAGTTGAAGAC  67 2667
    969954 N/A N/A  6407  6422 GTCCTTCAGATTTACA 117 2668
    969964 N/A N/A  6771  6786 ATACATGTCTGGTTTA  96 2669
    969974 511 526  6990  7005 TTTTGGCTCCCTCAGG 103 2670
    969984 N/A N/A  7169  7184 TTTCAACTTGTGACCC  99 2671
    969994 N/A N/A  7222  7237 ATACATTGAGGCATAC  98 2672
    970004 N/A N/A  7577  7592 GACATAAAGGACCCCG  92 2673
    970014 N/A N/A  7639  7654 GGTCTGAGTTGTACAG  80 2674
    970024 N/A N/A  8104  8119 CACCAATGGCAGCACC  84 2675
    970034 N/A N/A  8221  8236 CATGATAAGGCACTAC 106 2676
    970044 N/A N/A  8384  8399 TGGAGATACTTGTACT  58 2677
    970054 N/A N/A  8489  8504 ATCCCTTATTAGACTG 107 2678
    970064  645  660  9135  9150 CCAGCTTCGGTCGAGG 105 2679
    970074  701  716  9191  9206 GTCATGGGACATTGGT  74 2680
    970084 N/A N/A  9431  9446 CTGAGAGTAAACTTGG 101 2681
    970094 N/A N/A  9582  9597 GCTCAATAATCTCCCA 100 2682
    970104 N/A N/A  9679  9694 GTGTTTGCCATGGTAT  43 2683
    970114 N/A N/A  9842  9857 CGCATTGCTAGATTCT  63 2684
    970124 N/A N/A  9987 10002 GGATAACCTGAACATG  91 2685
    970134 N/A N/A 10120 10135 CCATATTGGAAACCAG  90 2686
    970144 N/A N/A 10178 10193 CAGTAAACGCAAGTCT 114 2687
    970154 N/A N/A 10262 10277 AGACAGGTCTCTACCT 112 2688
    970164 N/A N/A 10449 10464 TGCCAAAGAGCCCAAT 119 2689
    970174 N/A N/A 10675 10690 AACTAGCAGGGCACGC  98 2690
    970184  811  826 10876 10891 GGACTCCGGGAGCCTG 108 2691
    970194 N/A N/A 11103 11118 TTTCTAATGGTGCTCC  96 2692
    970203 N/A N/A 11365 11380 AACTAATGTCCCCAGG 112 2693
    970213 N/A N/A 11452 11467 TTGTTTGCAAGCTATA  64 2694
    970223 N/A N/A 11540 11555 TTCTTTATAGTAGGTA  85 2695
    970233 N/A N/A 11664 11679 GAATTCCAAACCTTAA  96 2696
    970243 N/A N/A 11946 11961 ACACAAGTCTTAGGTG 253 2697
    970253 N/A N/A 12007 12022 TCAGAAATCACGAGGT  57 2698
    970263 N/A N/A 12213 12228 TAATCTGTATCATGCA  78 2699
    970273 N/A N/A 12293 12308 AGCTGCCACTGGTAAC 100 2700
    970283 N/A N/A 12676 12691 GGCCTTAATGGTGATT 116 2701
    970293 N/A N/A 12929 12944 GAAATGAACCCTAAGT 105 2702
    970303 N/A N/A 13129 13144 ACCGACTCTTTTTTTA 102 2703
    970313 N/A N/A 13400 13415 CAGAGCTCCGGAGTCA 106 2704
    970323 N/A N/A 14015 14030 GCGACTGCTGAAAACC 104 2705
    970333 N/A N/A 14206 14221 AGTACAGTCCACTCCA  93 2706
    970343 N/A N/A 14248 14263 CCAACTTATAGCACTC  86 2707
    970353 N/A N/A 14673 14688 ACAAAAACTTGGGTCA 113 2708
    970363 N/A N/A 15188 15203 GATGGGACCGCCCTGG 113 2709
    970373 N/A N/A 15597 15612 CTAGTCGCGCAAGTCT 104 2710
    970383 N/A N/A 15852 15867 CAGAATGGCGAGTTGG  69 2711
    970393 N/A N/A 15918 15933 CTTAGTCAGAATCTGT  99 2712
    970403 N/A N/A 16174 16189 TAAAATGTCACGCCCG 100 2713
    970413 N/A N/A 16468 16483 CACCAGCCATCGGCAG 119 2714
    970423 N/A N/A 16699 16714 AGTGAAGTCGGGAGAT  92 2715
    970433 N/A N/A 16869 16884 GGCTCTTGATGTGAAC 112 2716
    970443 N/A N/A 16961 16976 ATCACCGAACACACCA 112 2717
  • TABLE 44
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID: SEQ ID: SEQ ID: IRF4 SEQ
    Compound 1 Start 1 Stop 2 Start 2 Stop (% ID
    Number Site Site Site Site Sequence UTC) NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT  26  195
    935583 N/A N/A 11119 11134 AGCAGTGATGTCAGGT  16 2718
    969845 N/A N/A  4005  4020 GCCAAGGAGGCGGGCC 102 2719
    969855 N/A N/A  4294  4309 ACCCAAATGTGGAGCT  97 2720
    969865 N/A N/A  4377  4392 GGAGAGGGCGACGACA 101 2721
    969875 N/A N/A  4541  4556 GAATAGGACCCCTATC 103 2722
    969885 N/A N/A  4876  4891 TCCGAGCTCGGCCCCC 110 2723
    969895 N/A N/A  5506  5521 TGCGGCTCCGGCGACG 120 2724
    969905 N/A N/A  5670  5685 AAACGAGAACGCACGG  91 2725
    969915 N/A N/A  5766  5781 CGCCGGCACAGGCGCG  86 2726
    969925 N/A N/A  6006  6021 GTGTGTGCACTCGCGC  81 2727
    969935 N/A N/A  6269  6284 AGATGCGGAGGTTCCT  68 2728
    969945 N/A N/A  6324  6339 CCTATCACTGCCAAGT 103 2729
    969955 N/A N/A  6412  6427 CATAGGTCCTTCAGAT 105 2730
    969965  414  429  6893  6908 CAAAGCGCACCGCAGG 104 2731
    969975 N/A N/A  6999  7014 CCCTACCTTTTTTGGC 107 2732
    969985 N/A N/A  7186  7201 GCTGAACCCCACAGGA 100 2733
    969995 N/A N/A  7223  7238 TATACATTGAGGCATA  93 2734
    970005 N/A N/A  7579  7594 GTGACATAAAGGACCC  90 2735
    970015 N/A N/A  7641  7656 AAGGTCTGAGTTGTAC  80 2736
    970025 N/A N/A  8130  8145 CCCGACCCTCCCCAAC 135 2737
    970035 N/A N/A  8223  8238 CACATGATAAGGCACT  79 2738
    970045 N/A N/A  8387  8402 CAATGGAGATACTTGT 116 2739
    970055 N/A N/A  8493  8508 GGGAATCCCTTATTAG 100 2740
    970065  647  662  9137  9152 CTCCAGCTTCGGTCGA  91 2741
    970075 N/A N/A  9280  9295 AGCAATTAGCTCTTCT  89 2742
    970085 N/A N/A  9435  9450 GATCCTGAGAGTAAAC  94 2743
    970095 N/A N/A  9583  9598 AGCTCAATAATCTCCC  94 2744
    970105 N/A N/A  9740  9755 CCACAATCAGCAAGTC 100 2745
    970115 N/A N/A  9844  9859 ACCGCATTGCTAGATT  73 2746
    970125 N/A N/A  9995 10010 GCAGCCAAGGATAACC  94 2747
    970135 N/A N/A 10127 10142 TCCACTACCATATTGG 129 2748
    970145 N/A N/A 10180 10195 AGCAGTAAACGCAAGT  73 2749
    970155 N/A N/A 10268 10283 GCTTCAAGACAGGTCT  71 2750
    970165 N/A N/A 10477 10492 GCTGAGAGTTCAGGTC  93 2751
    970175 N/A N/A 10678 10693 AGCAACTAGCAGGGCA 102 2752
    970185 N/A N/A 11001 11016 TCGAATCTGCCCAAAG  77 2753
    970204 N/A N/A 11369 11384 CCAGAACTAATGTCCC  94 2754
    970214 N/A N/A 11455 11470 TATTTGTTTGCAAGCT  70 2755
    970224 N/A N/A 11549 11564 AGAGGTGCCTTCTTTA  82 2756
    970234 N/A N/A 11749 11764 CCACAACTCTCGCCTC 109 2757
    970244 N/A N/A 11948 11963 CCACACAAGTCTTAGG  85 2758
    970254 N/A N/A 12048 12063 CGAGGTGATTCTCGGG  85 2759
    970264 N/A N/A 12222 12237 GCTGATAATTAATCTG 109 2760
    970274 N/A N/A 12373 12388 CGCCCATGAGTTGAAA  87 2761
    970284 N/A N/A 12692 12707 AAAGGGTAAGCACTGA  81 2762
    970294 N/A N/A 12991 13006 ATTTAAGTCATGTGTC  83 2763
    970304 N/A N/A 13132 13147 GCCACCGACTCTTTTT 105 2764
    970314 N/A N/A 13416 13431 CGGCAGTCTGCAAACA  76 2765
    970324 N/A N/A 14016 14031 GGCGACTGCTGAAAAC 110 2766
    970334 N/A N/A 14207 14222 CAGTACAGTCCACTCC  95 2767
    970344 N/A N/A 14249 14264 GCCAACTTATAGCACT  62 2768
    970354 N/A N/A 14686 14701 TCTGGATGAGCTTACA  86 2769
    970364 N/A N/A 15375 15390 ATCCACTGGCACCAAG  95 2770
    970374 N/A N/A 15599 15614 TTCTAGTCGCGCAAGT 107 2771
    970384 N/A N/A 15866 15881 CTACACAGGCTAATCA  96 2772
    970394 N/A N/A 15920 15935 GACTTAGTCAGAATCT  90 2773
    970404 N/A N/A 16176 16191 AATAAAATGTCACGCC  80 2774
    970414 N/A N/A 16610 16625 CAGAATGTTTCGACAT  86 2775
    970424 N/A N/A 16703 16718 CCACAGTGAAGTCGGG  94 2776
    970434 N/A N/A 16885 16900 TTACTCCGCTGAGTGG 104 2777
    970444 N/A N/A 16964 16979 CTCATCACCGAACACA  92 2778
  • TABLE 45
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID: SEQ ID: SEQ ID: IRF4 SEQ
    Compound 1 Start 1 Stop 2 Start 2 Stop (% ID
    Number Site Site Site Site Sequence UTC) NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT  33  195
    969846 N/A N/A  4037  4052 GCGCGGAGGGCAGGCG 132 2779
    969856 N/A N/A  4298  4313 AGCGACCCAAATGTGG 102 2780
    969866 N/A N/A  4407  4422 GCCCGGGAGAGCGGAG 132 2781
    969876 N/A N/A  4637  4652 CGCGGAGGACCTCGCC 107 2782
    969886 N/A N/A  4896  4911 GCGGGCACAGCCGTCC 121 2783
    969896 N/A N/A  5530  5545 AGCCGAGGCCTCCTTT 128 2784
    969906 N/A N/A  5673  5688 TGGAAACGAGAACGCA 107 2785
    969916 N/A N/A  5774  5789 AAAACAGCCGCCGGCA 109 2786
    969926 N/A N/A  6022  6037 CGTAACAACGACACAC 135 2787
    969936 N/A N/A  6272  6287 GTGAGATGCGGAGGTT  61 2788
    969946 N/A N/A  6360  6375 AGCTATGCTCTAGGAA  89 2789
    969956 N/A N/A  6414  6429 CGCATAGGTCCTTCAG  94 2790
    969966  429  444  6908  6923 GTCATTGCTCTTGTTC  82 2791
    969976 N/A N/A  7004  7019 AGAGCCCCTACCTTTT 107 2792
    969986 N/A N/A  7188  7203 ATGCTGAACCCCACAG  84 2793
    969996 N/A N/A  7224  7239 ATATACATTGAGGCAT 131 2794
    970006 N/A N/A  7592  7607 GCGAATGTGCCTTGTG  88 2795
    970016 N/A N/A  7644  7659 TACAAGGTCTGAGTTG 106 2796
    970026 N/A N/A  8132  8147 CGCCCGACCCTCCCCA 124 2797
    970036 N/A N/A  8224  8239 TCACATGATAAGGCAC  81 2798
    970046 N/A N/A  8390  8405 GGACAATGGAGATACT  97 2799
    970056 N/A N/A  8496  8511 TCAGGGAATCCCTTAT  96 2800
    970066  650  665  9140  9155 TCCCTCCAGCTTCGGT 121 2801
    970076 N/A N/A  9284  9299 CATTAGCAATTAGCTC 137 2802
    970086 N/A N/A  9437  9452 TGGATCCTGAGAGTAA 100 2803
    970096 N/A N/A  9587  9602 TACCAGCTCAATAATC 127 2804
    970106 N/A N/A  9744  9759 TAATCCACAATCAGCA 127 2805
    970116 N/A N/A  9847  9862 GTTACCGCATTGCTAG  84 2806
    970126 N/A N/A 10002 10017 ACTACCTGCAGCCAAG  96 2807
    970136 N/A N/A 10130 10145 TCCTCCACTACCATAT 113 2808
    970146 N/A N/A 10184 10199 CCAGAGCAGTAAACGC  89 2809
    970156 N/A N/A 10273 10288 CCGATGCTTCAAGACA  87 2810
    970166 N/A N/A 10489 10504 GTTCACAACAGAGCTG 116 2811
    970176 N/A N/A 10711 10726 CGCCCAATCACCTTCC 119 2812
    970186 N/A N/A 11005 11020 CCCATCGAATCTGCCC 124 2813
    970195 N/A N/A 11127 11142 GAACCACAAGCAGTGA 132 2814
    970205 N/A N/A 11371 11386 GACCAGAACTAATGTC 127 2815
    970215 N/A N/A 11468 11483 CAGATTGAATCCATAT  80 2816
    970225 N/A N/A 11553 11568 GCCTAGAGGTGCCTTC  87 2817
    970235 N/A N/A 11797 11812 AAAGAGCTGGTAGGTC 135 2818
    970245 N/A N/A 11960 11975 CTCTTCAGGCACCCAC  87 2819
    970255 N/A N/A 12052 12067 CATTCGAGGTGATTCT  89 2820
    970265 N/A N/A 12224 12239 TGGCTGATAATTAATC 105 2821
    970275 N/A N/A 12383 12398 TTTAAAATATCGCCCA 101 2822
    970285 N/A N/A 12694 12709 TTAAAGGGTAAGCACT 118 2823
    970295 N/A N/A 13039 13054 ACTTGCTAAGTCTTAT  87 2824
    970305 N/A N/A 13197 13212 TGGAGAAGTCCCGTGG 109 2825
    970315 N/A N/A 13769 13784 CCTTACCTGACAAGAA 111 2826
    970325 N/A N/A 14019 14034 AGAGGCGACTGCTGAA 119 2827
    970335 N/A N/A 14208 14223 CCAGTACAGTCCACTC 106 2828
    970345 N/A N/A 14332 14347 CGCTGAATTGTCATGA 101 2829
    970355 N/A N/A 14688 14703 AATCTGGATGAGCTTA  96 2830
    970365 N/A N/A 15410 15425 TCATTAGAAAGCCCTC 119 2831
    970375 N/A N/A 15602 15617 AAGTTCTAGTCGCGCA  89 2832
    970385 N/A N/A 15868 15883 ACCTACACAGGCTAAT 104 2833
    970395 N/A N/A 15986 16001 GCTAACTTACAGGACT 108 2834
    970405 N/A N/A 16252 16267 AGACAAGTGCCCATCC  99 2835
    970415 N/A N/A 16611 16626 TCAGAATGTTTCGACA  94 2836
    970425 N/A N/A 16712 16727 GGTAGTAGACCACAGT  77 2837
    970435 N/A N/A 16890 16905 CACTCTTACTCCGCTG 112 2838
    970445 N/A N/A 16966 16981 CCCTCATCACCGAACA 125 2839
  • TABLE 46
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: SEQ ID: SEQ ID: SEQ ID: IRF4 SEQ
    Compound 1 Start 1 Stop 2 Start 2 Stop (% ID
    Number Site Site Site Site Sequence UTC) NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT  33  195
    969847 N/A N/A  4044  4059 CGCAGGAGCGCGGAGG 128 2840
    969857 N/A N/A  4302  4317 TCGGAGCGACCCAAAT  88 2841
    969867 N/A N/A  4444  4459 ATTCCGCGCGCAGAGC 121 2842
    969877 N/A N/A  4643  4658 TCCACGCGCGGAGGAC 143 2843
    969887 N/A N/A  4928  4943 ACCTTCGCGGCCGGCC 142 2844
    969897 N/A N/A  5570  5585 CGCCCAGGACCCGGCT 101 2845
    969907 N/A N/A  5705  5720 CGGGAGCCCGGAGGAA 103 2846
    969917 N/A N/A  5782  5797 GAGAGACGAAAACAGC  95 2847
    969927 N/A N/A  6112  6127 GAGGAAGTCCCCTTCC  96 2848
    969937 N/A N/A  6274  6289 GAGTGAGATGCGGAGG  45 2849
    969947 N/A N/A  6364  6379 CCCCAGCTATGCTCTA 130 2850
    969957 N/A N/A  6416  6431 GGCGCATAGGTCCTTC 107 2851
    969967  446  461  6925  6940 TCAACCAGTTCCTCAA 123 2852
    969977 N/A N/A  7008  7023 CAGGAGAGCCCCTACC 108 2853
    969987 N/A N/A  7191  7206 CCTATGCTGAACCCCA 112 2854
    969997 N/A N/A  7225  7240 CATATACATTGAGGCA  80 2855
    970007 N/A N/A  7598  7613 TGGCATGCGAATGTGC 121 2856
    970017 N/A N/A  7648  7663 TTTCTACAAGGTCTGA  97 2857
    970027 N/A N/A  8135  8150 ACACGCCCGACCCTCC  96 2858
    970037 N/A N/A  8231  8246 TGTGGTTTCACATGAT  79 2859
    970047 N/A N/A  8403  8418 GGAGGATCATAAAGGA  68 2860
    970057 N/A N/A  8520  8535 GTGCTCTTACAGCCTC 115 2861
    970067  655  670  9145  9160 CGTAGTCCCTCCAGCT  73 2862
    970077 N/A N/A  9289  9304 GGCCACATTAGCAATT 100 2863
    970087 N/A N/A  9440  9455 GCATGGATCCTGAGAG  89 2864
    970097 N/A N/A  9600  9615 TTCGAGAGAAATATAC  78 2865
    970107 N/A N/A  9748  9763 CATCTAATCCACAATC 119 2866
    970117 N/A N/A  9849  9864 GAGTTACCGCATTGCT  53 2867
    970127 N/A N/A 10004 10019 TCACTACCTGCAGCCA  94 2868
    970137 N/A N/A 10133 10148 AATTCCTCCACTACCA 141 2869
    970147 N/A N/A 10187 10202 GAGCCAGAGCAGTAAA 102 2870
    970157 N/A N/A 10275 10290 TACCGATGCTTCAAGA 103 2871
    970167 N/A N/A 10499 10514 CACAAAGCGGGTTCAC 112 2872
    970177 N/A N/A 10777 10792 AGAGAGTCCGACGCAC 118 2873
    970187 N/A N/A 11006 11021 TCCCATCGAATCTGCC 105 2874
    970196 N/A N/A 11136 11151 CGGTCAGCAGAACCAC 108 2875
    970206 N/A N/A 11377 11392 ATGAGGGACCAGAACT  94 2876
    970216 N/A N/A 11470 11485 ATCAGATTGAATCCAT  77 2877
    970226 N/A N/A 11555 11570 AAGCCTAGAGGTGCCT  71 2878
    970236 N/A N/A 11813 11828 CCTCATTCACAACTAG  95 2879
    970246 N/A N/A 11963 11978 CTACTCTTCAGGCACC  82 2880
    970256 N/A N/A 12055 12070 GGCCATTCGAGGTGAT  99 2881
    970266 N/A N/A 12229 12244 GCTCATGGCTGATAAT 117 2882
    970276 N/A N/A 12385 12400 TCTTTAAAATATCGCC 145 2883
    970286 N/A N/A 12697 12712 ACATTAAAGGGTAAGC 123 2884
    970296 N/A N/A 13042 13057 AGAACTTGCTAAGTCT 134 2885
    970306 N/A N/A 13207 13222 GGTCAACACTTGGAGA 123 2886
    970316 N/A N/A 13771 13786 TGCCTTACCTGACAAG  96 2887
    970326 N/A N/A 14023 14038 TTTAAGAGGCGACTGC 200 2888
    970336 N/A N/A 14211 14226 AAACCAGTACAGTCCA 123 2889
    970346 N/A N/A 14431 14446 CCCACGCGGGAGGCTC 123 2890
    970356 N/A N/A 14706 14721 CTTTGGGCACCAAAAG 133 2891
    970366 N/A N/A 15411 15426 TTCATTAGAAAGCCCT 122 2892
    970376 N/A N/A 15606 15621 TAGTAAGTTCTAGTCG 113 2893
    970386 N/A N/A 15878 15893 CTGAGACTACACCTAC 140 2894
    970396 N/A N/A 15991 16006 TTCTAGCTAACTTACA 118 2895
    970406 N/A N/A 16271 16286 GACTGGAACATTGTTG 141 2896
    970416 N/A N/A 16639 16654 TGCCATGGACAAGTTT 118 2897
    970426 N/A N/A 16717 16732 CAAAAGGTAGTAGACC  89 2898
    970436 N/A N/A 16891 16906 GCACTCTTACTCCGCT  98 2899
    970446 N/A N/A 16970 16985 GAAACCCTCATCACCG 138 2900
  • TABLE 47
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence (% UTC) ID NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT  23  195
    969848 N/A N/A  4047  4062 CGTCGCAGGAGCGCGG  99 2901
    969858 N/A N/A  4313  4328 GCACGCAAGGCTCGGA  93 2902
    969868 N/A N/A  4446  4461 GGATTCCGCGCGCAGA  79 2903
    969878 N/A N/A  4677  4692 CGCGACTCTGTCAGTT  92 2904
    969888 N/A N/A  4981  4996 CTGCGAAGCGCGCGCG 106 2905
    969898 N/A N/A  5600  5615 GCCTTCAGCGGTTTCC  96 2906
    969908 N/A N/A  5719  5734 ACGGAGGCGGCAGACG 109 2907
    969918 N/A N/A  5785  5800 GGTGAGAGACGAAAAC 116 2908
    969928 N/A N/A  6115  6130 CCGGAGGAAGTCCCCT 100 2909
    969938 N/A N/A  6277  6292 GTAGAGTGAGATGCGG  49 2910
    969948 N/A N/A  6397  6412 TTTACACCGTTGCTCA  97 2911
    969958 N/A N/A  6418  6433 ATGGCGCATAGGTCCT 105 2912
    969968  450  465  6929  6944 CCGCTCAACCAGTTCC 112 2913
    969978 N/A N/A  7011  7026 ATTCAGGAGAGCCCCT 115 2914
    969988 N/A N/A  7193  7208 CTCCTATGCTGAACCC  91 2915
    969998 N/A N/A  7227  7242 CCCATATACATTGAGG  84 2916
    970008 N/A N/A  7603  7618 ACAGATGGCATGCGAA  81 2917
    970018 N/A N/A  7666  7681 TGCTATTAAACTGATT 103 2918
    970028 N/A N/A  8138  8153 CGGACACGCCCGACCC  93 2919
    970038 N/A N/A  8331  8346 ACCAAAAGTACCACAG 108 2920
    970048 N/A N/A  8445  8460 GACTGGAGTGAACCCT  62 2921
    970058 N/A N/A  8522  8537 GGGTGCTCTTACAGCC 102 2922
    970068  677  692  9167  9182 TCCGGGTGTGGCTGAT  74 2923
    970078 N/A N/A  9310  9325 CCAGGATTCGCCATGG  87 2924
    970088 N/A N/A  9445  9460 GCCTAGCATGGATCCT 104 2925
    970098 N/A N/A  9605  9620 CACTATTCGAGAGAAA  70 2926
    970108 N/A N/A  9754  9769 GGACCACATCTAATCC 112 2927
    970118 N/A N/A  9852  9867 CCTGAGTTACCGCATT  76 2928
    970128 N/A N/A 10011 10026 CACCTCTTCACTACCT 100 2929
    970138 N/A N/A 10138 10153 TAGCCAATTCCTCCAC  99 2930
    970148 N/A N/A 10193 10208 TCCATAGAGCCAGAGC  80 2931
    970158 N/A N/A 10277 10292 GTTACCGATGCTTCAA  54 2932
    970168 N/A N/A 10550 10565 ACTAACAGGGAGACTG 119 2933
    970178 N/A N/A 10779 10794 ACAGAGAGTCCGACGC 108 2934
    970188 N/A N/A 11012 11027 CTAAAGTCCCATCGAA 102 2935
    970197 N/A N/A 11142 11157 CTGAAACGGTCAGCAG  97 2936
    970207 N/A N/A 11399 11414 TAGGCACATCAATGTT  88 2937
    970217 N/A N/A 11525 11540 AAGATCTCCATGGTGC  61 2938
    970227 N/A N/A 11557 11572 CCAAGCCTAGAGGTGC  79 2939
    970237 N/A N/A 11820 11835 GTGCAAGCCTCATTCA  81 2940
    970247 N/A N/A 11993 12008 GTTGCCGAGATATAAA  87 2941
    970257 N/A N/A 12085 12100 AGACAGTGCGCCCCAA 117 2942
    970267 N/A N/A 12231 12246 GTGCTCATGGCTGATA  76 2943
    970277 N/A N/A 12455 12470 TAAAACTGCGCTCTCT 114 2944
    970287 N/A N/A 12860 12875 CCACATACCTGAAACG 109 2945
    970297 N/A N/A 13056 13071 GAGCATCACTATTAAG  86 2946
    970307 N/A N/A 13216 13231 CATGAGCTCGGTCAAC 101 2947
    970317 N/A N/A 13779 13794 TAACGAGGTGCCTTAC  87 2948
    970327 N/A N/A 14026 14041 TGTTTTAAGAGGCGAC  97 2949
    970337 N/A N/A 14217 14232 TGTGCAAAACCAGTAC 120 2950
    970347 N/A N/A 14448 14463 GGGTAGAGCAGCTCCC 116 2951
    970357 N/A N/A 14710 14725 TTTGCTTTGGGCACCA  76 2952
    970367 N/A N/A 15431 15446 TGCCAGTTCCTTGTGA 102 2953
    970377 N/A N/A 15607 15622 ATAGTAAGTTCTAGTC  89 2954
    970387 N/A N/A 15880 15895 ATCTGAGACTACACCT 108 2955
    970397 N/A N/A 16095 16110 ATACACACCCTCGGGC 110 2956
    970407 N/A N/A 16274 16289 ACGGACTGGAACATTG  62 2957
    970417 N/A N/A 16640 16655 ATGCCATGGACAAGTT  82 2958
    970427 N/A N/A 16728 16743 CCACGAAGATTCAAAA 107 2959
    970437 N/A N/A 16894 16909 TGAGCACTCTTACTCC 106 2960
    970447 N/A N/A 16976 16991 TGTTCAGAAACCCTCA 115 2961
  • TABLE 48
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence (% UTC) ID NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT  27  195
    969849 N/A N/A  4081  4096 CGGTTAGCTCATCCCG  95 2962
    969859 N/A N/A  4320  4335 GGCCACCGCACGCAAG 124 2963
    969869 N/A N/A  4488  4503 CGACAAGTGGCGCAGA  98 2964
    969879 N/A N/A  4805  4820 CGACACGCGCCGCTCG  62 2965
    969889 N/A N/A  4989  5004 CTTTGAGGCTGCGAAG  98 2966
    969899 N/A N/A  5610  5625 GCCCGGCCGGGCCTTC 104 2967
    969909 N/A N/A  5725  5740 CCACGGACGGAGGCGG 106 2968
    969919 N/A N/A  5793  5808 AGAGACGCGGTGAGAG 120 2969
    969929 N/A N/A  6123  6138 CCAAATTCCCGGAGGA 125 2970
    969939 N/A N/A  6280  6295 CCGGTAGAGTGAGATG 103 2971
    969949 N/A N/A  6398  6413 ATTTACACCGTTGCTC  87 2972
    969959 N/A N/A  6420  6435 GAATGGCGCATAGGTC  74 2973
    969969  454  469  6933  6948 GGCTCCGCTCAACCAG  91 2974
    969979 N/A N/A  7026  7041 TGTTAGGTGACCCAAA  98 2975
    969989 N/A N/A  7198  7213 TAATTCTCCTATGCTG  97 2976
    969999 N/A N/A  7243  7258 ATTCAATGCACCCCCC  98 2977
    970009 N/A N/A  7604  7619 GACAGATGGCATGCGA  84 2978
    970019 N/A N/A  7727  7742 ATAACACGGTGTTGAC  79 2979
    970029 N/A N/A  8140  8155 GGCGGACACGCCCGAC  93 2980
    970039 N/A N/A  8343  8358 GCTAAACCTGGCACCA  93 2981
    970049 N/A N/A  8451  8466 CGAAAAGACTGGAGTG  74 2982
    970059 N/A N/A  8784  8799 GGGTTAAAGGAGTGCA 100 2983
    970069  681  696  9171  9186 GATTTCCGGGTGTGGC  25 2984
    970079 N/A N/A  9371  9386 CCCCGAGCTGCACACG 105 2985
    970089 N/A N/A  9457  9472 ACGAAGGGCAGTGCCT 105 2986
    970099 N/A N/A  9613  9628 GAACACACCACTATTC 120 2987
    970109 N/A N/A  9772  9787 GGAACTCCCGAGGGCA  87 2988
    970119 N/A N/A  9854  9869 GGCCTGAGTTACCGCA  92 2989
    970129 N/A N/A 10013 10028 TACACCTCTTCACTAC 118 2990
    970139 N/A N/A 10143 10158 TATGTTAGCCAATTCC  59 2991
    970149 N/A N/A 10196 10211 AATTCCATAGAGCCAG  82 2992
    970159 N/A N/A 10279 10294 CTGTTACCGATGCTTC  44 2993
    970169 N/A N/A 10558 10573 TGTAACTGACTAACAG 131 2994
    970179 N/A N/A 10783 10798 CTAGACAGAGAGTCCG  95 2995
    970189 N/A N/A 11017 11032 AGTGTCTAAAGTCCCA  58 2996
    970198 N/A N/A 11143 11158 GCTGAAACGGTCAGCA  92 2997
    970208 N/A N/A 11401 11416 CTTAGGCACATCAATG  92 2998
    970218 N/A N/A 11527 11542 GTAAGATCTCCATGGT  83 2999
    970228 N/A N/A 11566 11581 GTGTGCTTGCCAAGCC  34 3000
    970238 N/A N/A 11826 11841 AAAAAGGTGCAAGCCT  94 3001
    970248 N/A N/A 11996 12011 GAGGTTGCCGAGATAT  71 3002
    970258 N/A N/A 12094 12109 AAGCGAGTCAGACAGT 122 3003
    970268 N/A N/A 12278 12293 CTGTATGGAACCCCAA  97 3004
    970278 N/A N/A 12511 12526 ATGTAAAGTCTGCTGA  80 3005
    970288 N/A N/A 12862 12877 GTCCACATACCTGAAA  92 3006
    970298 N/A N/A 13059 13074 ATAGAGCATCACTATT 100 3007
    970308 N/A N/A 13219 13234 CAGCATGAGCTCGGTC  78 3008
    970318 N/A N/A 13786 13801 TAACAGATAACGAGGT  88 3009
    970328 N/A N/A 14054 14069 TCGAGATCATAGTGCA  71 3010
    970338 N/A N/A 14219 14234 CCTGTGCAAAACCAGT 110 3011
    970348 N/A N/A 14459 14474 TGGCGAGTGGCGGGTA 118 3012
    970358 N/A N/A 14733 14748 AAGCTTAGTTATCTGG  65 3013
    970368 N/A N/A 15573 15588 AGGACACTCACAGGCG  92 3014
    970378 N/A N/A 15614 15629 CAGATTAATAGTAAGT 112 3015
    970388 N/A N/A 15885 15900 CCGTGATCTGAGACTA  55 3016
    970398 N/A N/A 16144 16159 TGACACAGGAGCCGCT  85 3017
    970408 N/A N/A 16283 16298 AGATACAAAACGGACT 115 3018
    970418 N/A N/A 16642 16657 TTATGCCATGGACAAG  81 3019
    970428 N/A N/A 16730 16745 ACCCACGAAGATTCAA 117 3020
    970438 N/A N/A 16899 16914 AGGAATGAGCACTCTT  93 3021
    970448 N/A N/A 16984 16999 AGAGACCATGTTCAGA  88 3022
    970608 1440 1455 19557 19572 AGATCTGTGGTAATCT 103 3023
  • TABLE 49
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence (% UTC) ID NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT  19  195
    969850 N/A N/A  4151  4166 GGCAGTTGTGCCGTCT 117 3024
    969860 N/A N/A  4342  4357 AGGGACCGCGCCAGGC 100 3025
    969870 N/A N/A  4490  4505 AACGACAAGTGGCGCA  88 3026
    969880 N/A N/A  4808  4823 TCCCGACACGCGCCGC 112 3027
    969890 N/A N/A  5006  5021 CCACGAGGCCCCGGAG  96 3028
    969900 N/A N/A  5655  5670 GACGAACGCGCAAAAC  85 3029
    969910 N/A N/A  5747  5762 GCACGGAGAGGGCGAG  96 3030
    969920 N/A N/A  5795  5810 ACAGAGACGCGGTGAG  86 3031
    969930 N/A N/A  6211  6226 GGACTAAGGACAGCTG  87 3032
    969940 N/A N/A  6283  6298 TAACCGGTAGAGTGAG  73 3033
    969950 N/A N/A  6400  6415 AGATTTACACCGTTGC  70 3034
    969960 N/A N/A  6423  6438 AAAGAATGGCGCATAG  90 3035
    969970  471  486  6950  6965 GTCTGAGATGTCCAGC  93 3036
    969980 N/A N/A  7156  7171 CCCACATAACTCAGGC 116 3037
    969990 N/A N/A  7201  7216 GATTAATTCTCCTATG 119 3038
    970000 N/A N/A  7375  7390 TGAGATATTCCTCTCA  82 3039
    970010 N/A N/A  7628  7643 TACAGGACAGGTAAAG 129 3040
    970020 N/A N/A  7735  7750 TAGAATGCATAACACG  92 3041
    970030 N/A N/A  8142  8157 CAGGCGGACACGCCCG 105 3042
    970040 N/A N/A  8346  8361 ATGGCTAAACCTGGCA  78 3043
    970050 N/A N/A  8453  8468 TCCGAAAAGACTGGAG 107 3044
    970060 N/A N/A  9095  9110 TGCTAAAGGAGTGCAG 117 3045
    970070  688  703  9178  9193 GGTACGGGATTTCCGG  88 3046
    970080 N/A N/A  9390  9405 AGTGAGAAAACCCCCC  92 3047
    970090 N/A N/A  9459  9474 CCACGAAGGGCAGTGC 100 3048
    970100 N/A N/A  9649  9664 TTTAGTATCACCTCTA  70 3049
    970110 N/A N/A  9795  9810 AGGGAGCTCATTTTGA 108 3050
    970120 N/A N/A  9857  9872 GAAGGCCTGAGTTACC  71 3051
    970130 N/A N/A 10022 10037 AAAGAGTGGTACACCT  90 3052
    970140 N/A N/A 10154 10169 GGAGCTAGTTTTATGT 128 3053
    970150 N/A N/A 10201 10216 TTACTAATTCCATAGA  97 3054
    970160 N/A N/A 10280 10295 ACTGTTACCGATGCTT  57 3055
    970170 N/A N/A 10561 10576 CTCTGTAACTGACTAA  84 3056
    970180 N/A N/A 10827 10842 TGTCACCTGGCAACCT 104 3057
    970190 N/A N/A 11019 11034 CAAGTGTCTAAAGTCC  97 3058
    970199 N/A N/A 11144 11159 GGCTGAAACGGTCAGC 127 3059
    970209 N/A N/A 11404 11419 ACTCTTAGGCACATCA  73 3060
    970219 N/A N/A 11529 11544 AGGTAAGATCTCCATG  68 3061
    970229 N/A N/A 11654 11669 CCTTAAGCTATTTGGT 886 3062
    970239 N/A N/A 11848 11863 GTTACTCACGAGCACC 117 3063
    970249 N/A N/A 11998 12013 ACGAGGTTGCCGAGAT  38 3064
    970259 N/A N/A 12098 12113 CTGAAAGCGAGTCAGA  94 3065
    970269 N/A N/A 12279 12294 ACTGTATGGAACCCCA  70 3066
    970279 N/A N/A 12513 12528 TCATGTAAAGTCTGCT  79 3067
    970289 N/A N/A 12876 12891 AAAGAAGCAAGTCGGT 102 3068
    970299 N/A N/A 13062 13077 ATTATAGAGCATCACT 106 3069
    970309 N/A N/A 13308 13323 CCACATGTCCCGTGGG 128 3070
    970319 N/A N/A 13788 13803 TCTAACAGATAACGAG 103 3071
    970329 N/A N/A 14089 14104 CCTGAAAAGAGCCGCC 103 3072
    970339 N/A N/A 14227 14242 TAACTTCTCCTGTGCA  85 3073
    970349 N/A N/A 14644 14659 GTACGAGCACATGTCA 100 3074
    970359 N/A N/A 14741 14756 CTGGCCTGAAGCTTAG  75 3075
    970369 N/A N/A 15587 15602 AAGTCTACAGCCCCAG 105 3076
    970379 N/A N/A 15668 15683 GCACAGCCCTTGGTTA  97 3077
    970389 N/A N/A 15890 15905 CACTGCCGTGATCTGA  91 3078
    970399 N/A N/A 16153 16168 GAAACGAGTTGACACA 100 3079
    970409 N/A N/A 16333 16348 CGCTTGTGGATATACA 100 3080
    970419 N/A N/A 16650 16665 AGACCAATTTATGCCA  93 3081
    970429 N/A N/A 16739 16754 CAGCATTGGACCCACG  96 3082
    970439 N/A N/A 16901 16916 AGAGGAATGAGCACTC  95 3083
    970449 N/A N/A 17002 17017 TGTAGAAGCCCACAAG 107 3084
    970609 1443 1458 19560 19575 GATAGATCTGTGGTAA  78 3085
  • TABLE 50
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence (% UTC) ID NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT  21  195
    969851 N/A N/A  4214  4229 GGAACGAAGAGCAGGG  88 3086
    969861 N/A N/A  4344  4359 GCAGGGACCGCGCCAG  90 3087
    969871 N/A N/A  4493  4508 GCAAACGACAAGTGGC 115 3088
    969881 N/A N/A  4823  4838 CCGCAGCCCAAAGGCT  96 3089
    969891 N/A N/A  5046  5061 CGCACTCCGGGCACCC  89 3090
    969901 N/A N/A  5658  5673 ACGGACGAACGCGCAA 107 3091
    969911 N/A N/A  5751  5766 GGACGCACGGAGAGGG  85 3092
    969921 N/A N/A  5799  5814 AGAAACAGAGACGCGG  89 3093
    969931 N/A N/A  6213  6228 TAGGACTAAGGACAGC 105 3094
    969941 N/A N/A  6288  6303 ATTTATAACCGGTAGA  72 3095
    969951 N/A N/A  6401  6416 CAGATTTACACCGTTG  85 3096
    969961 N/A N/A  6540  6555 GCATAGGCATCCTTCC  92 3097
    969971 474 489  6953  6968 CGGGTCTGAGATGTCC 102 3098
    969981 N/A N/A  7160  7175 GTGACCCACATAACTC  93 3099
    969991 N/A N/A  7205  7220 GTGTGATTAATTCTCC  36 3100
    970001 N/A N/A  7377  7392 GATGAGATATTCCTCT 124 3101
    970011 N/A N/A  7630  7645 TGTACAGGACAGGTAA  92 3102
    970021 N/A N/A  7783  7798 ACCTAACTAAATGTCA 124 3103
    970031 N/A N/A  8149  8164 ATTCCAACAGGCGGAC  98 3104
    970041 N/A N/A  8348  8363 ATATGGCTAAACCTGG  82 3105
    970051 N/A N/A  8454  8469 ATCCGAAAAGACTGGA 120 3106
    970061 N/A N/A  9103  9118 TGTGAACCTGCTAAAG 110 3107
    970071  690  705  9180  9195 TTGGTACGGGATTTCC  66 3108
    970081 N/A N/A  9412  9427 TGGGATGCCACCATCC 102 3109
    970091 N/A N/A  9466  9481 TAAGATCCCACGAAGG  91 3110
    970101 N/A N/A  9659  9674 CCGTTCCTTTTTTAGT 103 3111
    970111 N/A N/A  9834  9849 TAGATTCTCCCTGCAC  82 3112
    970121 N/A N/A  9914  9929 GTTCAGTGTGTTGACC  70 3113
    970131 N/A N/A 10100 10115 TGCTGCAAATCCCTCT  79 3114
    970141 N/A N/A 10159 10174 TTTCAGGAGCTAGTTT  92 3115
    970151 N/A N/A 10206 10221 CATGGTTACTAATTCC  75 3116
    970161 N/A N/A 10281 10296 TACTGTTACCGATGCT  63 3117
    970171 N/A N/A 10568 10583 GCGCTCTCTCTGTAAC 107 3118
    970181  763  778 10828 10843 CTGTCACCTGGCAACC  89 3119
    970191 N/A N/A 11085 11100 AATCACCCTGGTCACC  99 3120
    970200 N/A N/A 11334 11349 ACTTATTTGTGGCTCA  64 3121
    970210 N/A N/A 11407 11422 ATTACTCTTAGGCACA  70 3122
    970220 N/A N/A 11531 11546 GTAGGTAAGATCTCCA  78 3123
    970230 N/A N/A 11656 11671 AACCTTAAGCTATTTG  49 3124
    970240 N/A N/A 11851 11866 TCAGTTACTCACGAGC 103 3125
    970250 N/A N/A 12002 12017 AATCACGAGGTTGCCG 106 3126
    970260 N/A N/A 12149 12164 TTTGAGACTTAACCCA  69 3127
    970270 N/A N/A 12281 12296 TAACTGTATGGAACCC  72 3128
    970280 N/A N/A 12590 12605 CTGGATATGTGGTGTT  70 3129
    970290 N/A N/A 12892 12907 TATAACGGTGTTTCAG  64 3130
    970300 N/A N/A 13066 13081 TCCTATTATAGAGCAT  97 3131
    970310 N/A N/A 13352 13367 AACGACTCCACAGAGC  96 3132
    970320 N/A N/A 13880 13895 GCCGAAGTCAACAGGA 117 3133
    970330 N/A N/A 14115 14130 TCCAACCTTTATGATT 103 3134
    970340 N/A N/A 14229 14244 TATAACTTCTCCTGTG  93 3135
    970350 N/A N/A 14647 14662 GAAGTACGAGCACATG  82 3136
    970360 N/A N/A 14988 15003 CAGCACCGTGGTGCGA 127 3137
    970370 N/A N/A 15589 15604 GCAAGTCTACAGCCCC  51 3138
    970380 N/A N/A 15801 15816 ATAACATGAGAGTGTT 117 3139
    970390 N/A N/A 15892 15907 CACACTGCCGTGATCT  80 3140
    970400 N/A N/A 16156 16171 AAAGAAACGAGTTGAC  86 3141
    970410 N/A N/A 16379 16394 AGTAACTTGACTTGAG 103 3142
    970420 N/A N/A 16658 16673 ATGGCAAAAGACCAAT 105 3143
    970430 N/A N/A 16746 16761 TGCTTTGCAGCATTGG  70 3144
    970440 N/A N/A 16927 16942 AGCTTACTGTGATTCT  87 3145
    970450 1250 1265 17043 17058 CTTGGCAGGGAGCGGC  75 3146
    970610 1445 1460 19562 19577 CGGATAGATCTGTGGT  54 3147
  • TABLE 51
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence (% UTC) ID NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT  28  195
    969852 N/A N/A  4219  4234 CCTTAGGAACGAAGAG 106 3148
    969862 N/A N/A  4346  4361 AGGCAGGGACCGCGCC 111 3149
    969872 N/A N/A  4495  4510 CTGCAAACGACAAGTG 118 3150
    969882 N/A N/A  4829  4844 ACGCACCCGCAGCCCA 110 3151
    969892 N/A N/A  5052  5067 AGGCACCGCACTCCGG 113 3152
    969902 N/A N/A  5661  5676 CGCACGGACGAACGCG 117 3153
    969912 N/A N/A  5753  5768 GCGGACGCACGGAGAG 109 3154
    969922 N/A N/A  5878  5893 GCTAGCAGGAGCGAGA 105 3155
    969932 N/A N/A  6215  6230 CCTAGGACTAAGGACA 103 3156
    969942 N/A N/A  6291  6306 GGTATTTATAACCGGT  90 3157
    969952 N/A N/A  6402  6417 TCAGATTTACACCGTT  86 3158
    969962 N/A N/A  6543  6558 GTTGCATAGGCATCCT  73 3159
    969972  483  498  6962  6977 CACTTTGTACGGGTCT  89 3160
    969982 N/A N/A  7164  7179 ACTTGTGACCCACATA 104 3161
    969992 N/A N/A  7207  7222 CAGTGTGATTAATTCT  83 3162
    970002 N/A N/A  7563  7578 CGCCAGCCAGATGTTT 115 3163
    970012 N/A N/A  7632  7647 GTTGTACAGGACAGGT  67 3164
    970022 N/A N/A  7792  7807 CAGGAACTGACCTAAC 107 3165
    970032 N/A N/A  8152  8167 CATATTCCAACAGGCG 101 3166
    970042 N/A N/A  8351  8366 GTCATATGGCTAAACC  77 3167
    970052 N/A N/A  8478  8493 GACTGACAGCCGAAGC  73 3168
    970062  626  641  9116  9131 GGCATCATGTAGTTGT 101 3169
    970072  693  708  9183  9198 ACATTGGTACGGGATT  98 3170
    970082 N/A N/A  9420  9435 CTTGGCTGTGGGATGC  79 3171
    970092 N/A N/A  9469  9484 AAATAAGATCCCACGA 107 3172
    970102 N/A N/A  9668  9683 GGTATTTTTCCGTTCC  70 3173
    970112 N/A N/A  9836  9851 GCTAGATTCTCCCTGC 113 3174
    970122 N/A N/A  9922  9937 TCCAAAGGGTTCAGTG  93 3175
    970132 N/A N/A 10104 10119 CCCTTGCTGCAAATCC 104 3176
    970142 N/A N/A 10173 10188 AACGCAAGTCTGAATT  97 3177
    970152 N/A N/A 10209 10224 TCCCATGGTTACTAAT 110 3178
    970162 N/A N/A 10286 10301 TCATTTACTGTTACCG  44 3179
    970172  769  784 10604 10619 AACGAGCCAGTGCACA 101 3180
    970182 N/A N/A 10834 10849 AGGTTCCTGTCACCTG 107 3181
    970192 N/A N/A 11095 11110 GGTGCTCCTAAATCAC 101 3182
    970201 N/A N/A 11335 11350 GACTTATTTGTGGCTC  80 3183
    970211 N/A N/A 11410 11425 TGTATTACTCTTAGGC  35 3184
    970221 N/A N/A 11538 11553 CTTTATAGTAGGTAAG 101 3185
    970231 N/A N/A 11658 11673 CAAACCTTAAGCTATT  66 3186
    970241 N/A N/A 11928 11943 CAAGACAAGGGTTTGA 103 3187
    970251 N/A N/A 12003 12018 AAATCACGAGGTTGCC  79 3188
    970261 N/A N/A 12208 12223 TGTATCATGCATACCA  97 3189
    970271 N/A N/A 12285 12300 CTGGTAACTGTATGGA  83 3190
    970281 N/A N/A 12591 12606 ACTGGATATGTGGTGT  90 3191
    970291 N/A N/A 12894 12909 AATATAACGGTGTTTC  92 3192
    970301 N/A N/A 13111 13126 GAACAAGTGTATCTTT  95 3193
    970311 N/A N/A 13370 13385 GGACACCACCTCGAGG  99 3194
    970321 N/A N/A 13912 13927 TCTACTGGAGTCAAGC  70 3195
    970331 N/A N/A 14194 14209 TCCACCCTCCGTCTCA 109 3196
    970341 N/A N/A 14231 14246 CCTATAACTTCTCCTG 107 3197
    970351 N/A N/A 14650 14665 CCAGAAGTACGAGCAC 103 3198
    970361 N/A N/A 14990 15005 TGCAGCACCGTGGTGC 101 3199
    970371 N/A N/A 15592 15607 CGCGCAAGTCTACAGC  87 3200
    970381 N/A N/A 15812 15827 TCCAACCCTAGATAAC 105 3201
    970391 N/A N/A 15894 15909 TTCACACTGCCGTGAT 112 3202
    970401 N/A N/A 16161 16176 CCGCAAAAGAAACGAG 107 3203
    970411 N/A N/A 16386 16401 ATGGAACAGTAACTTG  97 3204
    970421 N/A N/A 16666 16681 GTCACGCAATGGCAAA 102 3205
    970431 N/A N/A 16770 16785 AACTAGTCGACAGCTA 107 3206
    970441 N/A N/A 16933 16948 AGCAAGAGCTTACTGT 106 3207
    970451 1254 1269 17047 17062 GAATCTTGGCAGGGAG 100 3208
    970611 1451 1466 19568 19583 GAATGGCGGATAGATC 103 3209
  • TABLE 52
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence (% UTC) ID NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT  27  195
    969853 N/A N/A  4221  4236 CCCCTTAGGAACGAAG 106 3210
    969863 N/A N/A  4362  4377 AGCTGCGGAGCCTGGG  69 3211
    969873 N/A N/A  4499  4514 GGCTCTGCAAACGACA 100 3212
    969883 N/A N/A  4833  4848 TGTAACGCACCCGCAG 104 3213
    969893 N/A N/A  5464  5479 GTCCGCCCCGCGCGGT  97 3214
    969903 N/A N/A  5665  5680 AGAACGCACGGACGAA  99 3215
    969913 N/A N/A  5756  5771 GGCGCGGACGCACGGA  90 3216
    969923 N/A N/A  5996  6011 TCGCGCAAAGGGCAAG 104 3217
    969933 N/A N/A  6264  6279 CGGAGGTTCCTTGAGG  58 3218
    969943 N/A N/A  6293  6308 TGGGTATTTATAACCG  96 3219
    969953 N/A N/A  6405  6420 CCTTCAGATTTACACC 109 3220
    969963 N/A N/A  6545  6560 ATGTTGCATAGGCATC  90 3221
    969973 489 504  6968  6983 CCTGTACACTTTGTAC 102 3222
    969983 N/A N/A  7167  7182 TCAACTTGTGACCCAC  86 3223
    969993 N/A N/A  7216  7231 TGAGGCATACAGTGTG  82 3224
    970003 N/A N/A  7575  7590 CATAAAGGACCCCGCC 105 3225
    970013 N/A N/A  7636  7651 CTGAGTTGTACAGGAC  45 3226
    970023 N/A N/A  8100  8115 AATGGCAGCACCGTGT 100 3227
    970033 N/A N/A  8216  8231 TAAGGCACTACTTCCA  90 3228
    970043 N/A N/A  8382  8397 GAGATACTTGTACTGT  51 3229
    970053 N/A N/A  8480  8495 TAGACTGACAGCCGAA  97 3230
    970063  630  645  9120  9135 GGGTGGCATCATGTAG  73 3231
    970073  699  714  9189  9204 CATGGGACATTGGTAC  82 3232
    970083 N/A N/A  9429  9444 GAGAGTAAACTTGGCT  88 3233
    970093 N/A N/A  9552  9567 TATTTATGAGCTTCCA  79 3234
    970103 N/A N/A  9671  9686 CATGGTATTTTTCCGT  62 3235
    970113 N/A N/A  9838  9853 TTGCTAGATTCTCCCT  84 3236
    970123 N/A N/A  9927  9942 AAACATCCAAAGGGTT 101 3237
    970133 N/A N/A 10106 10121 AGCCCTTGCTGCAAAT 111 3238
    970143 N/A N/A 10176 10191 GTAAACGCAAGTCTGA  86 3239
    970153 N/A N/A 10212 10227 CTTTCCCATGGTTACT  92 3240
    970163 N/A N/A 10306 10321 CACCTGATCTTGCTGC  88 3241
    970173 N/A N/A 10613 10628 TGATGGAGAAACGAGC 102 3242
    970183  772  787 10837 10852 AAAAGGTTCCTGTCAC 105 3243
    970193 N/A N/A 11100 11115 CTAATGGTGCTCCTAA  96 3244
    970202 N/A N/A 11338 11353 GAGGACTTATTTGTGG  78 3245
    970212 N/A N/A 11412 11427 TGTGTATTACTCTTAG  25 3246
    970222 N/A N/A 11539 11554 TCTTTATAGTAGGTAA  86 3247
    970232 N/A N/A 11662 11677 ATTCCAAACCTTAAGC 101 3248
    970242 N/A N/A 11931 11946 GTTCAAGACAAGGGTT  85 3249
    970252 N/A N/A 12006 12021 CAGAAATCACGAGGTT  75 3250
    970262 N/A N/A 12211 12226 ATCTGTATCATGCATA  76 3251
    970272 N/A N/A 12291 12306 CTGCCACTGGTAACTG  79 3252
    970282 N/A N/A 12657 12672 GGGTGGTAGAATGTGA  67 3253
    970292 N/A N/A 12926 12941 ATGAACCCTAAGTTTA 104 3254
    970302 N/A N/A 13114 13129 AAGGAACAAGTGTATC  87 3255
    970312 N/A N/A 13395 13410 CTCCGGAGTCAGTGCT  99 3256
    970322 N/A N/A 13961 13976 GACCATCTGATCCGGA  98 3257
    970332 N/A N/A 14203 14218 ACAGTCCACTCCACCC  86 3258
    970342 N/A N/A 14245 14260 ACTTATAGCACTCTCC  99 3259
    970352 N/A N/A 14669 14684 AAACTTGGGTCACTTA  95 3260
    970362 N/A N/A 15148 15163 CTTAGAATGAGAGGTG  99 3261
    970372 N/A N/A 15595 15610 AGTCGCGCAAGTCTAC 100 3262
    970382 N/A N/A 15846 15861 GGCGAGTTGGCACAAT  51 3263
    970392 N/A N/A 15896 15911 CATTCACACTGCCGTG  94 3264
    970402 N/A N/A 16163 16178 GCCCGCAAAAGAAACG  98 3265
    970412 N/A N/A 16416 16431 TCTGAGTAGACTTCTT  86 3266
    970422 N/A N/A 16670 16685 CGTAGTCACGCAATGG  85 3267
    970432 N/A N/A 16772 16787 GGAACTAGTCGACAGC  82 3268
    970442 N/A N/A 16958 16973 ACCGAACACACCAGGT 114 3269
    970452 1277 1292 17070 17085 TCTCCAAAGCATAGAG 108 3270
    970612 1465 1480 19582 19597 ATTCTTGAATAGAGGA  84 3271
  • Example 10: Effect of Mixed MOE and cEt Gapmers with Phosphorothioate Internucleoside Linkages on Human IRF4 In Vitro, Single Dose
  • Modified oligonucleotides complementary to a human IRF4 nucleic acid were designed and tested for their effect on IRF4 mRNA in vitro.
  • Cultured MM.1R cells at a density of 5,000 cells per well were transfected by free uptake with 1,000 nM concentration of modified oligonucleotide or no modified oligonucleotide for untreated controls. After approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by quantitative real-time PCR. Human primer probe set hIRF4_LTS34726 (described hereinabove in Example 7) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN®. Results are presented in the tables below as percent control of the amount of IRF4 mRNA, relative to untreated control (UTC) cells.
  • The modified oligonucleotides in Tables 53 through 58 are cEt and/or MOE containing gapmers. The modified oligonucleotides have a central gap segment comprising 2′-deoxynucleosides which is flanked by wing segments on the 5′ direction and the 3′ direction. At least one nucleoside in the 5′ wing segment and/or one nucleoside in the 3′ wing segment has a MOE and/or cEt sugar modification. The “Motif” column describes the sugar modifications of each oligonucleotide. “k” indicates a cEt sugar modification; “d” indicates deoxyribose; and “c” indicates a MOE modification. Each internucleoside linkage is a phosphorothioate internucleoside linkage and each cytosine residue is a 5-methylcytosine. “Start Site” indicates the 5′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence. “Stop Site” indicates the 3′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Each modified oligonucleotide listed in Tables 53 through 58 below is complementary to human IRF4 nucleic acid sequences SEQ ID NO: 1 or SEQ ID NO: 2, as indicated. ‘N/A’ indicates that the modified oligonucleotide is not complementary to that particular nucleic acid sequence with 100% complementarity. As shown below, modified oligonucleotides complementary to human IRF4 reduced the amount of human IRF4 mRNA.
  • TABLE 53
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence Motif (% UTC) ID NO
     609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT kkk-d10-kkk  13  195
     881450 3252 3267 21369 21384 ACACTTTTAGAGAGGA kkk-d10-kkk  27 2111
     881659 4592 4607 22709 22724 GGAAGTTTACACTGGA kkk-d10-kkk   4 2044
    1013023 N/A N/A 10142 10157 ATGTTAGCCAATTCCT k-d10-kekek 100 3272
    1013024 N/A N/A 10143 10158 TATGTTAGCCAATTCC k-d10-kekek  99 2991
    1013025 N/A N/A 10144 10159 TTATGTTAGCCAATTC k-d10-kekek  98 3273
    1013026 N/A N/A 10145 10160 TTTATGTTAGCCAATT k-d10-kekek 100 3274
    1013032 N/A N/A 10278 10293 TGTTACCGATGCTTCA k-d10-kekek  74 2294
    1013033 N/A N/A 10279 10294 CTGTTACCGATGCTTC k-d10-kekek  64 2993
    1013034 N/A N/A 10280 10295 ACTGTTACCGATGCTT k-d10-kekek  80 3055
    1013035 N/A N/A 10281 10296 TACTGTTACCGATGCT k-d10-kekek  90 3117
    1013046 N/A N/A 11016 11031 GTGTCTAAAGTCCCAT k-d10-kekek  66 3275
    1013047 N/A N/A 11017 11032 AGTGTCTAAAGTCCCA k-d10-kekek 101 2996
    1013048 N/A N/A 11018 11033 AAGTGTCTAAAGTCCC k-d10-kekek 101 3276
    1013049 N/A N/A 11019 11034 CAAGTGTCTAAAGTCC k-d10-kekek  93 3058
    1013053 N/A N/A 11119 11134 AGCAGTGATGTCAGGT k-d10-kekek  23 2718
    1013054 N/A N/A 11120 11135 AAGCAGTGATGTCAGG k-d10-kekek  72 3277
    1013055 N/A N/A 11121 11136 CAAGCAGTGATGTCAG k-d10-kekek  65 3278
    1013060 N/A N/A 11395 11410 CACATCAATGTTTTAG k-d10-kekek  55 3279
    1013061 N/A N/A 11396 11411 GCACATCAATGTTTTA k-d10-kekek  87 1159
    1013062 N/A N/A 11397 11412 GGCACATCAATGTTTT k-d10-kekek  72 3280
    1013063 N/A N/A 11398 11413 AGGCACATCAATGTTT k-d10-kekek  95 1233
    1013074 N/A N/A 11411 11426 GTGTATTACTCTTAGG k-d10-kekek  16 1540
    1013075 N/A N/A 11412 11427 TGTGTATTACTCTTAG k-d10-kekek  42 3246
    1013076 N/A N/A 11413 11428 ATGTGTATTACTCTTA k-d10-kekek  83 3281
    1013077 N/A N/A 11414 11429 AATGTGTATTACTCTT k-d10-kekek  76 3282
    1013090 N/A N/A 11565 11580 TGTGCTTGCCAAGCCT k-d10-kekek 101 3283
    1013091 N/A N/A 11566 11581 GTGTGCTTGCCAAGCC k-d10-kekek  60 3000
    1013092 N/A N/A 11567 11582 CGTGTGCTTGCCAAGC k-d10-kekek  70 3284
    1013093 N/A N/A 11568 11583 ACGTGTGCTTGCCAAG k-d10-kekek  53 3285
    1013125 N/A N/A 12514 12529 TTCATGTAAAGTCTGC k-d10-kekek  98 3286
    1013126 N/A N/A 12515 12530 GTTCATGTAAAGTCTG k-d10-kekek  55  934
    1013127 N/A N/A 12516 12531 AGTTCATGTAAAGTCT k-d10-kekek  75  755
    1013128 N/A N/A 12517 12532 AAGTTCATGTAAAGTC k-d10-kekek  86 3287
    1013462 N/A N/A 10142 10157 ATGTTAGCCAATTCCT kk-d9-kekek  72 3272
    1013463 N/A N/A 10143 10158 TATGTTAGCCAATTCC kk-d9-kekek  92 2991
    1013464 N/A N/A 10144 10159 TTATGTTAGCCAATTC kk-d9-kekek  89 3273
    1013465 N/A N/A 10145 10160 TTTATGTTAGCCAATT kk-d9-kekek  91 3274
    1013471 N/A N/A 10278 10293 TGTTACCGATGCTTCA kk-d9-kekek  72 2294
    1013472 N/A N/A 10279 10294 CTGTTACCGATGCTTC kk-d9-kekek  48 2993
    1013473 N/A N/A 10280 10295 ACTGTTACCGATGCTT kk-d9-kekek  70 3055
    1013474 N/A N/A 10281 10296 TACTGTTACCGATGCT kk-d9-kekek  91 3117
    1013485 N/A N/A 11016 11031 GTGTCTAAAGTCCCAT kk-d9-kekek  87 3275
    1013486 N/A N/A 11017 11032 AGTGTCTAAAGTCCCA kk-d9-kekek  74 2996
    1013487 N/A N/A 11018 11033 AAGTGTCTAAAGTCCC kk-d9-kekek  88 3276
    1013488 N/A N/A 11019 11034 CAAGTGTCTAAAGTCC kk-d9-kekek  85 3058
    1013492 N/A N/A 11119 11134 AGCAGTGATGTCAGGT kk-d9-kekek  34 2718
    1013493 N/A N/A 11120 11135 AAGCAGTGATGTCAGG kk-d9-kekek  57 3277
    1013494 N/A N/A 11121 11136 CAAGCAGTGATGTCAG kk-d9-kekek  49 3278
    1013499 N/A N/A 11395 11410 CACATCAATGTTTTAG kk-d9-kekek  81 3279
    1013500 N/A N/A 11396 11411 GCACATCAATGTTTTA kk-d9-kekek  82 1159
    1013501 N/A N/A 11397 11412 GGCACATCAATGTTTT kk-d9-kekek  77 3280
    1013502 N/A N/A 11398 11413 AGGCACATCAATGTTT kk-d9-kekek  84 1233
    1013513 N/A N/A 11411 11426 GTGTATTACTCTTAGG kk-d9-kekek  14 1540
    1013514 N/A N/A 11412 11427 TGTGTATTACTCTTAG kk-d9-kekek  13 3246
    1013515 N/A N/A 11413 11428 ATGTGTATTACTCTTA kk-d9-kekek  46 3281
    1013516 N/A N/A 11414 11429 AATGTGTATTACTCTT kk-d9-kekek  48 3282
    1013529 N/A N/A 11565 11580 TGTGCTTGCCAAGCCT kk-d9-kekek  98 3283
  • TABLE 54
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence Motif (% UTC) ID NO
     609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT kkk-d10-kkk 11  195
     881450 3252 3267 21369 21384 ACACTTTTAGAGAGGA kkk-d10-kkk 27 2111
     881659 4592 4607 22709 22724 GGAAGTTTACACTGGA kkk-d10-kkk  3 2044
    1013530 N/A N/A 11566 11581 GTGTGCTTGCCAAGCC kk-d9-kekek 59 3000
    1013531 N/A N/A 11567 11582 CGTGTGCTTGCCAAGC kk-d9-kekek 51 3284
    1013532 N/A N/A 11568 11583 ACGTGTGCTTGCCAAG kk-d9-kekek 51 3285
    1013564 N/A N/A 12514 12529 TTCATGTAAAGTCTGC kk-d9-kekek 90 3286
    1013565 N/A N/A 12515 12530 GTTCATGTAAAGTCTG kk-d9-kekek 58  934
    1013566 N/A N/A 12516 12531 AGTTCATGTAAAGTCT kk-d9-kekek 58  755
    1013567 N/A N/A 12517 12532 AAGTTCATGTAAAGTC kk-d9-kekek 66 3287
    1013902 N/A N/A 10142 10157 ATGTTAGCCAATTCCT kk-d10-keke 80 3272
    1013903 N/A N/A 10143 10158 TATGTTAGCCAATTCC kk-d10-keke 92 2991
    1013904 N/A N/A 10144 10159 TTATGTTAGCCAATTC kk-d10-keke 89 3273
    1013905 N/A N/A 10145 10160 TTTATGTTAGCCAATT kk-d10-keke 89 3274
    1013911 N/A N/A 10278 10293 TGTTACCGATGCTTCA kk-d10-keke 75 2294
    1013912 N/A N/A 10279 10294 CTGTTACCGATGCTTC kk-d10-keke 57 2993
    1013913 N/A N/A 10280 10295 ACTGTTACCGATGCTT kk-d10-keke 70 3055
    1013914 N/A N/A 10281 10296 TACTGTTACCGATGCT kk-d10-keke 76 3117
    1013925 N/A N/A 11016 11031 GTGTCTAAAGTCCCAT kk-d10-keke 91 3275
    1013926 N/A N/A 11017 11032 AGTGTCTAAAGTCCCA kk-d10-keke 68 2996
    1013927 N/A N/A 11018 11033 AAGTGTCTAAAGTCCC kk-d10-keke 90 3276
    1013928 N/A N/A 11019 11034 CAAGTGTCTAAAGTCC kk-d10-keke 84 3058
    1013932 N/A N/A 11119 11134 AGCAGTGATGTCAGGT kk-d10-keke 33 2718
    1013933 N/A N/A 11120 11135 AAGCAGTGATGTCAGG kk-d10-keke 26 3277
    1013934 N/A N/A 11121 11136 CAAGCAGTGATGTCAG kk-d10-keke 80 3278
    1013939 N/A N/A 11395 11410 CACATCAATGTTTTAG kk-d10-keke 75 3279
    1013940 N/A N/A 11396 11411 GCACATCAATGTTTTA kk-d10-keke 51 1159
    1013941 N/A N/A 11397 11412 GGCACATCAATGTTTT kk-d10-keke 91 3280
    1013942 N/A N/A 11398 11413 AGGCACATCAATGTTT kk-d10-keke 84 1233
    1013953 N/A N/A 11411 11426 GTGTATTACTCTTAGG kk-d10-keke 22 1540
    1013954 N/A N/A 11412 11427 TGTGTATTACTCTTAG kk-d10-keke 49 3246
    1013955 N/A N/A 11413 11428 ATGTGTATTACTCTTA kk-d10-keke 53 3281
    1013956 N/A N/A 11414 11429 AATGTGTATTACTCTT kk-d10-keke 92 3282
    1013969 N/A N/A 11565 11580 TGTGCTTGCCAAGCCT kk-d10-keke 74 3283
    1013970 N/A N/A 11566 11581 GTGTGCTTGCCAAGCC kk-d10-keke 63 3000
    1013971 N/A N/A 11567 11582 CGTGTGCTTGCCAAGC kk-d10-keke 45 3284
    1013972 N/A N/A 11568 11583 ACGTGTGCTTGCCAAG kk-d10-keke 94 3285
    1014004 N/A N/A 12514 12529 TTCATGTAAAGTCTGC kk-d10-keke 51 3286
    1014005 N/A N/A 12515 12530 GTTCATGTAAAGTCTG kk-d10-keke 69  934
    1014006 N/A N/A 12516 12531 AGTTCATGTAAAGTCT kk-d10-keke 55  755
    1014007 N/A N/A 12517 12532 AAGTTCATGTAAAGTC kk-d10-keke 72 3287
  • Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence Motif (% UTC) ID NO
     609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT kkk-d10-kkk  9  195
     881450 3252 3267 21369 21384 ACACTTTTAGAGAGGA kkk-d10-kkk 17 2111
     881659 4592 4607 22709 22724 GGAAGTTTACACTGGA kkk-d10-kkk  2 2044
    1014342 N/A N/A 10142 10157 ATGTTAGCCAATTCCT kk-d9-kdkdk 70 3272
    1014343 N/A N/A 10143 10158 TATGTTAGCCAATTCC kk-d9-kdkdk 98 2991
    1014344 N/A N/A 10144 10159 TTATGTTAGCCAATTC kk-d9-kdkdk 83 3273
    1014345 N/A N/A 10145 10160 TTTATGTTAGCCAATT kk-d9-kdkdk 89 3274
    1014351 N/A N/A 10278 10293 TGTTACCGATGCTTCA kk-d9-kdkdk 65 2294
    1014352 N/A N/A 10279 10294 CTGTTACCGATGCTTC kk-d9-kdkdk 42 2993
    1014353 N/A N/A 10280 10295 ACTGTTACCGATGCTT kk-d9-kdkdk 78 3055
    1014354 N/A N/A 10281 10296 TACTGTTACCGATGCT kk-d9-kdkdk 93 3117
    1014365 N/A N/A 11016 11031 GTGTCTAAAGTCCCAT kk-d9-kdkdk 80 3275
    1014366 N/A N/A 11017 11032 AGTGTCTAAAGTCCCA kk-d9-kdkdk 86 2996
    1014367 N/A N/A 11018 11033 AAGTGTCTAAAGTCCC kk-d9-kdkdk 87 3276
    1014368 N/A N/A 11019 11034 CAAGTGTCTAAAGTCC kk-d9-kdkdk 97 3058
    1014372 N/A N/A 11119 11134 AGCAGTGATGTCAGGT kk-d9-kdkdk 45 2718
    1014373 N/A N/A 11120 11135 AAGCAGTGATGTCAGG kk-d9-kdkdk 40 3277
    1014374 N/A N/A 11121 11136 CAAGCAGTGATGTCAG kk-d9-kdkdk 54 3278
    1014379 N/A N/A 11395 11410 CACATCAATGTTTTAG kk-d9-kdkdk 72 3279
    1014380 N/A N/A 11396 11411 GCACATCAATGTTTTA kk-d9-kdkdk 89 1159
    1014381 N/A N/A 11397 11412 GGCACATCAATGTTTT kk-d9-kdkdk 74 3280
    1014382 N/A N/A 11398 11413 AGGCACATCAATGTTT kk-d9-kdkdk 96 1233
    1014393 N/A N/A 11411 11426 GTGTATTACTCTTAGG kk-d9-kdkdk 11 1540
    1014394 N/A N/A 11412 11427 TGTGTATTACTCTTAG kk-d9-kdkdk 19 3246
    1014395 N/A N/A 11413 11428 ATGTGTATTACTCTTA kk-d9-kdkdk 56 3281
    1014396 N/A N/A 11414 11429 AATGTGTATTACTCTT kk-d9-kdkdk 90 3282
    1014409 N/A N/A 11565 11580 TGTGCTTGCCAAGCCT kk-d9-kdkdk 77 3283
    1014410 N/A N/A 11566 11581 GTGTGCTTGCCAAGCC kk-d9-kdkdk 41 3000
    1014411 N/A N/A 11567 11582 CGTGTGCTTGCCAAGC kk-d9-kdkdk 33 3284
    1014412 N/A N/A 11568 11583 ACGTGTGCTTGCCAAG kk-d9-kdkdk 25 3285
    1014444 N/A N/A 12514 12529 TTCATGTAAAGTCTGC kk-d9-kdkdk 86 3286
    1014445 N/A N/A 12515 12530 GTTCATGTAAAGTCTG kk-d9-kdkdk 66  934
    1014446 N/A N/A 12516 12531 AGTTCATGTAAAGTCT kk-d9-kdkdk 68  755
    1014447 N/A N/A 12517 12532 AAGTTCATGTAAAGTC kk-d9-kdkdk 68 3287
    1014783 N/A N/A 10142 10157 ATGTTAGCCAATTCCT kk-d9-eeekk 83 3272
    1014784 N/A N/A 10143 10158 TATGTTAGCCAATTCC kk-d9-eeekk 92 2991
    1014785 N/A N/A 10144 10159 TTATGTTAGCCAATTC kk-d9-eeekk 86 3273
    1014786 N/A N/A 10145 10160 TTTATGTTAGCCAATT kk-d9-eeekk 97 3274
    1014792 N/A N/A 10278 10293 TGTTACCGATGCTTCA kk-d9-eeekk 69 2294
    1014793 N/A N/A 10279 10294 CTGTTACCGATGCTTC kk-d9-eeekk 36 2993
    1014794 N/A N/A 10280 10295 ACTGTTACCGATGCTT kk-d9-eeekk 73 3055
    1014795 N/A N/A 10281 10296 TACTGTTACCGATGCT kk-d9-eeekk 71 3117
    1014806 N/A N/A 11016 11031 GTGTCTAAAGTCCCAT kk-d9-eeekk 77 3275
    1014807 N/A N/A 11017 11032 AGTGTCTAAAGTCCCA kk-d9-eeekk 74 2996
    1014808 N/A N/A 11018 11033 AAGTGTCTAAAGTCCC kk-d9-eeekk 79 3276
    1014809 N/A N/A 11019 11034 CAAGTGTCTAAAGTCC kk-d9-eeekk 78 3058
    1014813 N/A N/A 11119 11134 AGCAGTGATGTCAGGT kk-d9-eeekk 31 2718
    1014814 N/A N/A 11120 11135 AAGCAGTGATGTCAGG kk-d9-eeekk 38 3277
    1014815 N/A N/A 11121 11136 CAAGCAGTGATGTCAG kk-d9-eeekk 85 3278
    1014820 N/A N/A 11395 11410 CACATCAATGTTTTAG kk-d9-ceekk 88 3279
    1014821 N/A N/A 11396 11411 GCACATCAATGTTTTA kk-d9-ceekk 80 1159
    1014822 N/A N/A 11397 11412 GGCACATCAATGTTTT kk-d9-ceekk 78 3280
    1014823 N/A N/A 11398 11413 AGGCACATCAATGTTT kk-d9-eeekk 64 1233
    1014834 N/A N/A 11411 11426 GTGTATTACTCTTAGG kk-d9-eeekk 12 1540
  • TABLE 56
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence Motif (% UTC) ID NO
     609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT kkk-d10-kkk 14  195
     881450 3252 3267 21369 21384 ACACTTTTAGAGAGGA kkk-d10-kkk 24 2111
     881659 4592 4607 22709 22724 GGAAGTTTACACTGGA kkk-d10-kkk  2 2044
    1014835 N/A N/A 11412 11427 TGTGTATTACTCTTAG kk-d9-eeekk 59 3246
    1014836 N/A N/A 11413 11428 ATGTGTATTACTCTTA kk-d9-eeekk 60 3281
    1014837 N/A N/A 11414 11429 AATGTGTATTACTCTT kk-d9-eeekk 85 3282
    1014850 N/A N/A 11565 11580 TGTGCTTGCCAAGCCT kk-d9-eeekk 55 3283
    1014851 N/A N/A 11566 11581 GTGTGCTTGCCAAGCC kk-d9-eeekk 25 3000
    1014852 N/A N/A 11567 11582 CGTGTGCTTGCCAAGC kk-d9-eeekk 40 3284
    1014853 N/A N/A 11568 11583 ACGTGTGCTTGCCAAG kk-d9-eeekk 56 3285
    1014885 N/A N/A 12514 12529 TTCATGTAAAGTCTGC kk-d9-eeekk 73 3286
    1014886 N/A N/A 12515 12530 GTTCATGTAAAGTCTG kk-d9-eeekk 71  934
    1014887 N/A N/A 12516 12531 AGTTCATGTAAAGTCT kk-d9-eeekk 59  755
    1014888 N/A N/A 12517 12532 AAGTTCATGTAAAGTC kk-d9-eeekk 79 3287
    1015224 N/A N/A 10142 10157 ATGTTAGCCAATTCCT kk-d9-ekeke 73 3272
    1015225 N/A N/A 10143 10158 TATGTTAGCCAATTCC kk-d9-ekeke 98 2991
    1015226 N/A N/A 10144 10159 TTATGTTAGCCAATTC kk-d9-ekeke 91 3273
    1015227 N/A N/A 10145 10160 TTTATGTTAGCCAATT kk-d9-ekeke 88 3274
    1015233 N/A N/A 10278 10293 TGTTACCGATGCTTCA kk-d9-ekeke 65 2294
    1015234 N/A N/A 10279 10294 CTGTTACCGATGCTTC kk-d9-ekeke 50 2993
    1015235 N/A N/A 10280 10295 ACTGTTACCGATGCTT kk-d9-ekeke 77 3055
    1015236 N/A N/A 10281 10296 TACTGTTACCGATGCT kk-d9-ekeke 78 3117
    1015247 N/A N/A 11016 11031 GTGTCTAAAGTCCCAT kk-d9-ekeke 68 3275
    1015248 N/A N/A 11017 11032 AGTGTCTAAAGTCCCA kk-d9-ekeke 82 2996
    1015249 N/A N/A 11018 11033 AAGTGTCTAAAGTCCC kk-d9-ekeke 87 3276
    1015250 N/A N/A 11019 11034 CAAGTGTCTAAAGTCC kk-d9-ekeke 77 3058
    1015254 N/A N/A 11119 11134 AGCAGTGATGTCAGGT kk-d9-ekeke 28 2718
    1015255 N/A N/A 11120 11135 AAGCAGTGATGTCAGG kk-d9-ekeke 35 3277
    1015256 N/A N/A 11121 11136 CAAGCAGTGATGTCAG kk-d9-ekeke 74 3278
    1015261 N/A N/A 11395 11410 CACATCAATGTTTTAG kk-d9-ekeke 72 3279
    1015262 N/A N/A 11396 11411 GCACATCAATGTTTTA kk-d9-ekeke 90 1159
    1015263 N/A N/A 11397 11412 GGCACATCAATGTTTT kk-d9-ekeke 78 3280
    1015264 N/A N/A 11398 11413 AGGCACATCAATGTTT kk-d9-ekeke 58 1233
    1015275 N/A N/A 11411 11426 GTGTATTACTCTTAGG kk-d9-ekeke 11 1540
    1015276 N/A N/A 11412 11427 TGTGTATTACTCTTAG kk-d9-ekeke 46 3246
    1015277 N/A N/A 11413 11428 ATGTGTATTACTCTTA kk-d9-ekeke 40 3281
    1015278 N/A N/A 11414 11429 AATGTGTATTACTCTT kk-d9-ekeke 76 3282
    1015291 N/A N/A 11565 11580 TGTGCTTGCCAAGCCT kk-d9-ekeke 79 3283
    1015292 N/A N/A 11566 11581 GTGTGCTTGCCAAGCC kk-d9-ekeke 83 3000
    1015293 N/A N/A 11567 11582 CGTGTGCTTGCCAAGC kk-d9-ekeke 53 3284
    1015294 N/A N/A 11568 11583 ACGTGTGCTTGCCAAG kk-d9-ekeke 41 3285
    1015326 N/A N/A 12514 12529 TTCATGTAAAGTCTGC kk-d9-ekeke 68 3286
    1015327 N/A N/A 12515 12530 GTTCATGTAAAGTCTG kk-d9-ekeke 64  934
    1015328 N/A N/A 12516 12531 AGTTCATGTAAAGTCT kk-d9-ekeke 49  755
    1015329 N/A N/A 12517 12532 AAGTTCATGTAAAGTC kk-d9-ekeke 66 3287
  • TABLE 57
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence Motif (% UTC) ID NO
     609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT kkk-d10-kkk  18  195
     881450 3252 3267 21369 21384 ACACTTTTAGAGAGGA kkk-d10-kkk  28 2111
     881659 4592 4607 22709 22724 GGAAGTTTACACTGGA kkk-d10-kkk   4 2044
    1012810 N/A N/A 10142 10157 ATGTTAGCCAATTCCT kkk-d10-kkk  70 3272
    1012811 N/A N/A 10144 10159 TTATGTTAGCCAATTC kkk-d10-kkk  91 3273
    1012812 N/A N/A 10145 10160 TTTATGTTAGCCAATT kkk-d10-kkk  75 3274
    1012816 N/A N/A 11016 11031 GTGTCTAAAGTCCCAT kkk-d10-kkk  82 3275
    1012817 N/A N/A 11018 11033 AAGTGTCTAAAGTCCC kkk-d10-kkk  50 3276
    1012819 N/A N/A 11120 11135 AAGCAGTGATGTCAGG kkk-d10-kkk  34 3277
    1012820 N/A N/A 11121 11136 CAAGCAGTGATGTCAG kkk-d10-kkk  40 3278
    1012821 N/A N/A 11395 11410 CACATCAATGTTTTAG kkk-d10-kkk  34 3279
    1012822 N/A N/A 11397 11412 GGCACATCAATGTTTT kkk-d10-kkk  82 3280
    1012826 N/A N/A 11413 11428 ATGTGTATTACTCTTA kkk-d10-kkk  48 3281
    1012827 N/A N/A 11414 11429 AATGTGTATTACTCTT kkk-d10-kkk  47 3282
    1012835 N/A N/A 11565 11580 TGTGCTTGCCAAGCCT kkk-d10-kkk  62 3283
    1012836 N/A N/A 11567 11582 CGTGTGCTTGCCAAGC kkk-d10-kkk  33 3284
    1012837 N/A N/A 11568 11583 ACGTGTGCTTGCCAAG kkk-d10-kkk  46 3285
    1012845 N/A N/A 12514 12529 TTCATGTAAAGTCTGC kkk-d10-kkk  43 3286
    1012846 N/A N/A 12517 12532 AAGTTCATGTAAAGTC kkk-d10-kkk  57 3287
    1015665 N/A N/A 10142 10157 ATGTTAGCCAATTCCT k-d9-kekeke 100 3272
    1015666 N/A N/A 10143 10158 TATGTTAGCCAATTCC k-d9-kekeke  90 2991
    1015667 N/A N/A 10144 10159 TTATGTTAGCCAATTC k-d9-kekeke  91 3273
    1015668 N/A N/A 10145 10160 TTTATGTTAGCCAATT k-d9-kekeke  95 3274
    1015674 N/A N/A 10278 10293 TGTTACCGATGCTTCA k-d9-kekeke  90 2294
    1015675 N/A N/A 10279 10294 CTGTTACCGATGCTTC k-d9-kekeke  98 2993
    1015676 N/A N/A 10280 10295 ACTGTTACCGATGCTT k-d9-kekeke 102 3055
    1015677 N/A N/A 10281 10296 TACTGTTACCGATGCT k-d9-kekeke  82 3117
    1015688 N/A N/A 11016 11031 GTGTCTAAAGTCCCAT k-d9-kekeke  95 3275
    1015689 N/A N/A 11017 11032 AGTGTCTAAAGTCCCA k-d9-kekeke 112 2996
    1015690 N/A N/A 11018 11033 AAGTGTCTAAAGTCCC k-d9-kekeke  96 3276
    1015691 N/A N/A 11019 11034 CAAGTGTCTAAAGTCC k-d9-kekeke  89 3058
    1015695 N/A N/A 11119 11134 AGCAGTGATGTCAGGT k-d9-kekeke  74 2718
    1015696 N/A N/A 11120 11135 AAGCAGTGATGTCAGG k-d9-kekeke  66 3277
    1015697 N/A N/A 11121 11136 CAAGCAGTGATGTCAG k-d9-kekeke  90 3278
    1015702 N/A N/A 11395 11410 CACATCAATGTTTTAG k-d9-kekeke 102 3279
    1015703 N/A N/A 11396 11411 GCACATCAATGTTTTA k-d9-kekeke  83 1159
    1015704 N/A N/A 11397 11412 GGCACATCAATGTTTT k-d9-kekeke  91 3280
    1015705 N/A N/A 11398 11413 AGGCACATCAATGTTT k-d9-kekeke 109 1233
    1015716 N/A N/A 11411 11426 GTGTATTACTCTTAGG k-d9-kekeke  16 1540
    1015717 N/A N/A 11412 11427 TGTGTATTACTCTTAG k-d9-kekeke  68 3246
    1015718 N/A N/A 11413 11428 ATGTGTATTACTCTTA k-d9-kekeke  64 3281
    1015719 N/A N/A 11414 11429 AATGTGTATTACTCTT k-d9-kekeke  88 3282
    1015732 N/A N/A 11565 11580 TGTGCTTGCCAAGCCT k-d9-kekeke 103 3283
    1015733 N/A N/A 11566 11581 GTGTGCTTGCCAAGCC k-d9-kekeke  94 3000
    1015734 N/A N/A 11567 11582 CGTGTGCTTGCCAAGC k-d9-kekeke  76 3284
    1015735 N/A N/A 11568 11583 ACGTGTGCTTGCCAAG k-d9-kekeke  60 3285
    1015767 N/A N/A 12514 12529 TTCATGTAAAGTCTGC k-d9-kekeke  91 3286
    1015768 N/A N/A 12515 12530 GTTCATGTAAAGTCTG k-d9-kekeke  76  934
    1015769 N/A N/A 12516 12531 AGTTCATGTAAAGTCT k-d9-kekeke  71  755
    1015770 N/A N/A 12517 12532 AAGTTCATGTAAAGTC k-d9-kekeke  86 3287
  • TABLE 58
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence Motif (% UTC) ID NO
     609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT kkk-d10-kkk  11  195
     881450 3252 3267 21369 21384 ACACTTTTAGAGAGGA kkk-d10-kkk  29 2111
     881659 4592 4607 22709 22724 GGAAGTTTACACTGGA kkk-d10-kkk   4 2044
     935595 3075 3090 21192 21207 ACTAAGCTTGATAAAG kkk-d10-kkk  86 3288
     935607 4195 4210 22312 22327 AGTGTTCCAGGAGATA kkk-d10-kkk  20 3289
    1012769 N/A N/A  4810  4825 GCTCCCGACACGCGCC kkk-d10-kkk  97 3290
    1012772 N/A N/A  6267  6282 ATGCGGAGGTTCCTTG kkk-d10-kkk  53 3291
    1012774 N/A N/A  6271  6286 TGAGATGCGGAGGTTC kkk-d10-kkk  67 3292
    1012775 N/A N/A  6273  6288 AGTGAGATGCGGAGGT kkk-d10-kkk  35 3293
    1012776 N/A N/A  6275  6290 AGAGTGAGATGCGGAG kkk-d10-kkk  35 3294
    1012778 N/A N/A  6281  6296 ACCGGTAGAGTGAGAT kkk-d10-kkk  84 3295
    1012782 N/A N/A  7634  7649 GAGTTGTACAGGACAG kkk-d10-kkk  49 3296
    1012785 N/A N/A  7638  7653 GTCTGAGTTGTACAGG kkk-d10-kkk  48 3297
    1012786 N/A N/A  7640  7655 AGGTCTGAGTTGTACA kkk-d10-kkk  45 3298
    1012788 N/A N/A  8386  8401 AATGGAGATACTTGTA kkk-d10-kkk  74 3299
    1012790 N/A N/A  8389  8404 GACAATGGAGATACTT kkk-d10-kkk  67 3300
    1012791  678  693  9168  9183 TTCCGGGTGTGGCTGA kkk-d10-kkk  75 3301
    1012793  680  695  9170  9185 ATTTCCGGGTGTGGCT kkk-d10-kkk  93 3302
    1012795 N/A N/A  9667  9682 GTATTTTTCCGTTCCT kkk-d10-kkk  16 3303
    1012796 N/A N/A  9670  9685 ATGGTATTTTTCCGTT kkk-d10-kkk  68 3304
    1012799 N/A N/A  9677  9692 GTTTGCCATGGTATTT kkk-d10-kkk  59 3305
    1012804 N/A N/A  9840  9855 CATTGCTAGATTCTCC kkk-d10-kkk  82 3306
    1012806 N/A N/A  9846  9861 TTACCGCATTGCTAGA kkk-d10-kkk  87 3307
    1012808 N/A N/A  9851  9866 CTGAGTTACCGCATTG kkk-d10-kkk  51 3308
    1012809 N/A N/A 10139 10154 TTAGCCAATTCCTCCA kkk-d10-kkk  64 3309
    1012813 N/A N/A 10274 10289 ACCGATGCTTCAAGAC kkk-d10-kkk  69 3310
    1012814 N/A N/A 10276 10291 TTACCGATGCTTCAAG kkk-d10-kkk  84 3311
    1012815 N/A N/A 10282 10297 TTACTGTTACCGATGC kkk-d10-kkk  74 3312
    1012818 N/A N/A 11020 11035 GCAAGTGTCTAAAGTC kkk-d10-kkk  51 3313
    1012823 N/A N/A 11400 11415 TTAGGCACATCAATGT kkk-d10-kkk  88 3314
    1012825 N/A N/A 11406 11421 TTACTCTTAGGCACAT kkk-d10-kkk  56 3315
    1012828 N/A N/A 11523 11538 GATCTCCATGGTGCAG kkk-d10-kkk  78 3316
    1012831 N/A N/A 11530 11545 TAGGTAAGATCTCCAT kkk-d10-kkk  65 3317
    1012834 N/A N/A 11564 11579 GTGCTTGCCAAGCCTA kkk-d10-kkk  73 3318
    1012840 N/A N/A 11659 11674 CCAAACCTTAAGCTAT kkk-d10-kkk  82 3319
    1012841 N/A N/A 11663 11678 AATTCCAAACCTTAAG kkk-d10-kkk 102 3320
    1012843 N/A N/A 11995 12010 AGGTTGCCGAGATATA kkk-d10-kkk  46 3321
    1012844 N/A N/A 11997 12012 CGAGGTTGCCGAGATA kkk-d10-kkk  34 3322
    1012848 N/A N/A 14251 14266 GAGCCAACTTATAGCA kkk-d10-kkk  89 3323
    1012850 N/A N/A 14253 14268 CAGAGCCAACTTATAG kkk-d10-kkk  70 3324
    1012852 N/A N/A 14734 14749 GAAGCTTAGTTATCTG kkk-d10-kkk  55 3325
    1012855 N/A N/A 14739 14754 GGCCTGAAGCTTAGTT kkk-d10-kkk 105 3326
    1012859 N/A N/A 15594 15609 GTCGCGCAAGTCTACA kkk-d10-kkk  96 3327
    1012860 N/A N/A 15841 15856 GTTGGCACAATTCTCT kkk-d10-kkk  78 3328
    1012864 N/A N/A 15845 15860 GCGAGTTGGCACAATT kkk-d10-kkk  73 3329
    1012866 N/A N/A 15848 15863 ATGGCGAGTTGGCACA kkk-d10-kkk  51 3330
    1012867 N/A N/A 15850 15865 GAATGGCGAGTTGGCA kkk-d10-kkk  61 3331
    1012869 N/A N/A 15884 15899 CGTGATCTGAGACTAC kkk-d10-kkk  75 3332
    1012872 N/A N/A 15889 15904 ACTGCCGTGATCTGAG kkk-d10-kkk  66 3333
    1012920 1441 1456 19558 19573 TAGATCTGTGGTAATC kkk-d10-kkk  80 3334
    1012921 1450 1465 19567 19582 AATGGCGGATAGATCT kkk-d10-kkk  90 3335
  • Example 11: Effect of Mixed MOE and cEt Gapmers with Phosphorothioate Internucleoside Linkages on Human IRF4 In Vitro, Single Dose
  • Modified oligonucleotides complementary to a human IRF4 nucleic acid were designed and tested for their effect on IRF4 mRNA in vitro.
  • Cultured MM.1R cells at a density of 5,000 cells per well were transfected by free uptake with 1,000 nM concentration of modified oligonucleotide or no modified oligonucleotide for untreated controls. After approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by quantitative real-time PCR. Human primer probe set RTS4522 (forward sequence CGGAAATCCCGTACCAATGT, designated herein as SEQ ID NO: 3392; reverse sequence TGGCAACCATTTTCACAAGCT designated herein as SEQ ID NO: 3393; probe sequence TTTGGACCCCGCGGCCAC, designated herein as SEQ ID: 3394) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN®. Results are presented in the tables below as percent control of the amount of IRF4 mRNA, relative to untreated control (UTC) cells.
  • The modified oligonucleotides in Tables 59 through 64 are cEt and/or MOE containing gapmers. The modified oligonucleotides have a central gap segment comprising 2′-deoxynucleosides which is flanked by wing segments on the 5′ direction and the 3′ direction. At least one nucleoside in the 5′ wing segment and/or one nucleoside in the 3′ wing segment has a MOE and/or cEt sugar modification. The “Motif” column describes the sugar modifications of each oligonucleotide. “k” indicates a cEt sugar modification; “d” indicates deoxyribose; and “e” indicates a MOE modification. Each internucleoside linkage is a phosphorothioate internucleoside linkage and each cytosine residue is a 5-methylcytosine. “Start Site” indicates the 5′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence. “Stop Site” indicates the 3′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Each modified oligonucleotide listed in Table 59 through 64 below is complementary to human IRF4 nucleic acid sequences SEQ ID NO: 1 or SEQ ID NO: 2, as indicated. ‘N/A’ indicates that the modified oligonucleotide is not complementary to that particular nucleic acid sequence with 100% complementarity. As shown below, modified oligonucleotides complementary to human IRF4 reduced the amount of human IRF4 mRNA.
  • TABLE 59
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence Motif (% UTC) ID NO
     609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT kkk-d10-kkk  24  195
     881450 3252 3267 21369 21384 ACACTTTTAGAGAGGA kkk-d10-kkk  29 2111
     881659 4592 4607 22709 22724 GGAAGTTTACACTGGA kkk-d10-kkk  14 2044
    1013023 N/A N/A 10142 10157 ATGTTAGCCAATTCCT k-d10-kekek  93 3272
    1013024 N/A N/A 10143 10158 TATGTTAGCCAATTCC k-d10-kekek  99 2991
    1013025 N/A N/A 10144 10159 TTATGTTAGCCAATTC k-d10-kekek  94 3273
    1013026 N/A N/A 10145 10160 TTTATGTTAGCCAATT k-d10-kekek 112 3274
    1013032 N/A N/A 10278 10293 TGTTACCGATGCTTCA k-d10-kekek  82 2294
    1013033 N/A N/A 10279 10294 CTGTTACCGATGCTTC k-d10-kekek  74 2993
    1013034 N/A N/A 10280 10295 ACTGTTACCGATGCTT k-d10-kekek  80 3055
    1013035 N/A N/A 10281 10296 TACTGTTACCGATGCT k-d10-kekek  98 3117
    1013046 N/A N/A 11016 11031 GTGTCTAAAGTCCCAT k-d10-kekek  77 3275
    1013047 N/A N/A 11017 11032 AGTGTCTAAAGTCCCA k-d10-kekek  97 2996
    1013048 N/A N/A 11018 11033 AAGTGTCTAAAGTCCC k-d10-kekek 101 3276
    1013049 N/A N/A 11019 11034 CAAGTGTCTAAAGTCC k-d10-kekek  88 3058
    1013053 N/A N/A 11119 11134 AGCAGTGATGTCAGGT k-d10-kekek  33 2718
    1013054 N/A N/A 11120 11135 AAGCAGTGATGTCAGG k-d10-kekek  61 3277
    1013055 N/A N/A 11121 11136 CAAGCAGTGATGTCAG k-d10-kekek  57 3278
    1013060 N/A N/A 11395 11410 CACATCAATGTTTTAG k-d10-kekek  81 3279
    1013061 N/A N/A 11396 11411 GCACATCAATGTTTTA k-d10-kekek 100 1159
    1013062 N/A N/A 11397 11412 GGCACATCAATGTTTT k-d10-kekek  75 3280
    1013063 N/A N/A 11398 11413 AGGCACATCAATGTTT k-d10-kekek  95 1233
    1013074 N/A N/A 11411 11426 GTGTATTACTCTTAGG k-d10-kekek  20 1540
    1013075 N/A N/A 11412 11427 TGTGTATTACTCTTAG k-d10-kekek  44 3246
    1013076 N/A N/A 11413 11428 ATGTGTATTACTCTTA k-d10-kekek  96 3281
    1013077 N/A N/A 11414 11429 AATGTGTATTACTCTT k-d10-kekek  71 3282
    1013090 N/A N/A 11565 11580 TGTGCTTGCCAAGCCT k-d10-kekek  97 3283
    1013091 N/A N/A 11566 11581 GTGTGCTTGCCAAGCC k-d10-kekek  77 3000
    1013092 N/A N/A 11567 11582 CGTGTGCTTGCCAAGC k-d10-kekek  68 3284
    1013093 N/A N/A 11568 11583 ACGTGTGCTTGCCAAG k-d10-kekek  63 3285
    1013125 N/A N/A 12514 12529 TTCATGTAAAGTCTGC k-d10-kekek 118 3286
    1013126 N/A N/A 12515 12530 GTTCATGTAAAGTCTG k-d10-kekek  78  934
    1013127 N/A N/A 12516 12531 AGTTCATGTAAAGTCT k-d10-kekek  78  755
    1013128 N/A N/A 12517 12532 AAGTTCATGTAAAGTC k-d10-kekek  94 3287
    1013207 N/A N/A 18073 18088 GTTGGCTGGTCTTTGT k-d10-kekek  77 3336
    1013208 N/A N/A 18074 18089 GGTTGGCTGGTCTTTG k-d10-kekek  53 3337
    1013209 N/A N/A 18075 18090 TGGTTGGCTGGTCTTT k-d10-kekek  91 3338
    1013210 N/A N/A 18076 18091 TTGGTTGGCTGGTCTT k-d10-kekek  66 3339
    1013213 N/A N/A 18087 18102 TTATATACTGGTTGGT k-d10-kekek  78 1179
    1013214 N/A N/A 18088 18103 ATTATATACTGGTTGG k-d10-kekek  78 3340
    1013215 N/A N/A 18089 18104 GATTATATACTGGTTG k-d10-kekek  52 1254
    1013216 N/A N/A 18090 18105 GGATTATATACTGGTT k-d10-kekek  65 1330
    1013217 N/A N/A 18091 18106 GGGATTATATACTGGT k-d10-kekek  66 3341
    1013218 N/A N/A 18092 18107 TGGGATTATATACTGG k-d10-kekek  57 3342
    1013232 N/A N/A 18571 18586 TGATAGCTGAGCTGAT k-d10-kekek  78 2546
    1013233 N/A N/A 18572 18587 GTGATAGCTGAGCTGA k-d10-kekek  71 3343
    1013234 N/A N/A 18573 18588 TGTGATAGCTGAGCTG k-d10-kekek 102 3344
    1013235 N/A N/A 18574 18589 ATGTGATAGCTGAGCT k-d10-kekek 103 3345
    1013236 N/A N/A 18575 18590 GATGTGATAGCTGAGC k-d10-kekek  50 3346
    1013237 N/A N/A 18576 18591 TGATGTGATAGCTGAG k-d10-kekek  82 3347
    1013238 N/A N/A 18577 18592 TTGATGTGATAGCTGA k-d10-kekek  88 3348
    1013252 N/A N/A 18611 18626 AGTGACTTGCATCCAT k-d10-kekek  98 3349
    1013253 N/A N/A 18612 18627 CAGTGACTTGCATCCA k-d10-kekek  71 3350
    1013254 N/A N/A 18613 18628 ACAGTGACTTGCATCC k-d10-kekek 105 3351
    1013255 N/A N/A 18614 18629 GACAGTGACTTGCATC k-d10-kekek  92 3352
    1013462 N/A N/A 10142 10157 ATGTTAGCCAATTCCT kk-d9-kekek  56 3272
    1013463 N/A N/A 10143 10158 TATGTTAGCCAATTCC kk-d9-kekek  97 2991
    1013464 N/A N/A 10144 10159 TTATGTTAGCCAATTC kk-d9-kekek  81 3273
    1013465 N/A N/A 10145 10160 TTTATGTTAGCCAATT kk-d9-kekek  85 3274
    1013471 N/A N/A 10278 10293 TGTTACCGATGCTTCA kk-d9-kekek  79 2294
    1013472 N/A N/A 10279 10294 CTGTTACCGATGCTTC kk-d9-kekek  56 2993
    1013473 N/A N/A 10280 10295 ACTGTTACCGATGCTT kk-d9-kekek  82 3055
    1013474 N/A N/A 10281 10296 TACTGTTACCGATGCT kk-d9-kekek  73 3117
    1013485 N/A N/A 11016 11031 GTGTCTAAAGTCCCAT kk-d9-kekek  61 3275
    1013486 N/A N/A 11017 11032 AGTGTCTAAAGTCCCA kk-d9-kekek  91 2996
    1013487 N/A N/A 11018 11033 AAGTGTCTAAAGTCCC kk-d9-kekek  78 3276
    1013488 N/A N/A 11019 11034 CAAGTGTCTAAAGTCC kk-d9-kekek  94 3058
    1013492 N/A N/A 11119 11134 AGCAGTGATGTCAGGT kk-d9-kekek  33 2718
    1013493 N/A N/A 11120 11135 AAGCAGTGATGTCAGG kk-d9-kekek  56 3277
    1013494 N/A N/A 11121 11136 CAAGCAGTGATGTCAG kk-d9-kekek  48 3278
    1013499 N/A N/A 11395 11410 CACATCAATGTTTTAG kk-d9-kekek  66 3279
    1013500 N/A N/A 11396 11411 GCACATCAATGTTTTA kk-d9-kekek  85 1159
    1013501 N/A N/A 11397 11412 GGCACATCAATGTTTT kk-d9-kekek  81 3280
    1013502 N/A N/A 11398 11413 AGGCACATCAATGTTT kk-d9-kekek  81 1233
    1013513 N/A N/A 11411 11426 GTGTATTACTCTTAGG kk-d9-kekek  22 1540
    1013514 N/A N/A 11412 11427 TGTGTATTACTCTTAG kk-d9-kekek  21 3246
    1013515 N/A N/A 11413 11428 ATGTGTATTACTCTTA kk-d9-kekek  51 3281
    1013516 N/A N/A 11414 11429 AATGTGTATTACTCTT kk-d9-kekek  59 3282
    1013529 N/A N/A 11565 11580 TGTGCTTGCCAAGCCT kk-d9-kekek  82 3283
  • TABLE 60
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence Motif (% UTC) ID NO
     609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT kkk-d10-kkk  18  195
     881450 3252 3267 21369 21384 ACACTTTTAGAGAGGA kkk-d10-kkk  36 2111
     881659 4592 4607 22709 22724 GGAAGTTTACACTGGA kkk-d10-kkk  10 2044
    1013530 N/A N/A 11566 11581 GTGTGCTTGCCAAGCC kk-d9-kekek  61 3000
    1013531 N/A N/A 11567 11582 CGTGTGCTTGCCAAGC kk-d9-kekek  57 3284
    1013532 N/A N/A 11568 11583 ACGTGTGCTTGCCAAG kk-d9-kekek  56 3285
    1013564 N/A N/A 12514 12529 TTCATGTAAAGTCTGC kk-d9-kekek  88 3286
    1013565 N/A N/A 12515 12530 GTTCATGTAAAGTCTG kk-d9-kekek  66  934
    1013566 N/A N/A 12516 12531 AGTTCATGTAAAGTCT kk-d9-kekek  69  755
    1013567 N/A N/A 12517 12532 AAGTTCATGTAAAGTC kk-d9-kekek  73 3287
    1013646 N/A N/A 18073 18088 GTTGGCTGGTCTTTGT kk-d9-kekek  38 3336
    1013647 N/A N/A 18074 18089 GGTTGGCTGGTCTTTG kk-d9-kekek  33 3337
    1013648 N/A N/A 18075 18090 TGGTTGGCTGGTCTTT kk-d9-kekek  56 3338
    1013649 N/A N/A 18076 18091 TTGGTTGGCTGGTCTT kk-d9-kekek  35 3339
    1013652 N/A N/A 18087 18102 TTATATACTGGTTGGT kk-d9-kekek  50 1179
    1013653 N/A N/A 18088 18103 ATTATATACTGGTTGG kk-d9-kekek  48 3340
    1013654 N/A N/A 18089 18104 GATTATATACTGGTTG kk-d9-kekek  55 1254
    1013655 N/A N/A 18090 18105 GGATTATATACTGGTT kk-d9-kekek  35 1330
    1013656 N/A N/A 18091 18106 GGGATTATATACTGGT kk-d9-kekek  60 3341
    1013657 N/A N/A 18092 18107 TGGGATTATATACTGG kk-d9-kekek  58 3342
    1013672 N/A N/A 18572 18587 GTGATAGCTGAGCTGA kk-d9-kekek  61 3343
    1013673 N/A N/A 18573 18588 TGTGATAGCTGAGCTG kk-d9-kekek  83 3344
    1013674 N/A N/A 18574 18589 ATGTGATAGCTGAGCT kk-d9-kekek  76 3345
    1013675 N/A N/A 18575 18590 GATGTGATAGCTGAGC kk-d9-kekek  69 3346
    1013676 N/A N/A 18576 18591 TGATGTGATAGCTGAG kk-d9-kekek 102 3347
    1013677 N/A N/A 18577 18592 TTGATGTGATAGCTGA kk-d9-kekek  76 3348
    1013691 N/A N/A 18611 18626 AGTGACTTGCATCCAT kk-d9-kekek  73 3349
    1013692 N/A N/A 18612 18627 CAGTGACTTGCATCCA kk-d9-kekek  74 3350
    1013693 N/A N/A 18613 18628 ACAGTGACTTGCATCC kk-d9-kekek  68 3351
    1013694 N/A N/A 18614 18629 GACAGTGACTTGCATC kk-d9-kekek  95 3352
    1013902 N/A N/A 10142 10157 ATGTTAGCCAATTCCT kk-d10-keke  85 3272
    1013903 N/A N/A 10143 10158 TATGTTAGCCAATTCC kk-d10-keke  75 2991
    1013904 N/A N/A 10144 10159 TTATGTTAGCCAATTC kk-d10-keke  84 3273
    1013905 N/A N/A 10145 10160 TTTATGTTAGCCAATT kk-d10-keke 105 3274
    1013911 N/A N/A 10278 10293 TGTTACCGATGCTTCA kk-d10-keke  58 2294
    1013912 N/A N/A 10279 10294 CTGTTACCGATGCTTC kk-d10-keke  63 2993
    1013913 N/A N/A 10280 10295 ACTGTTACCGATGCTT kk-d10-keke  52 3055
    1013914 N/A N/A 10281 10296 TACTGTTACCGATGCT kk-d10-keke  83 3117
    1013925 N/A N/A 11016 11031 GTGTCTAAAGTCCCAT kk-d10-keke  94 3275
    1013926 N/A N/A 11017 11032 AGTGTCTAAAGTCCCA kk-d10-keke  61 2996
    1013927 N/A N/A 11018 11033 AAGTGTCTAAAGTCCC kk-d10-keke  88 3276
    1013928 N/A N/A 11019 11034 CAAGTGTCTAAAGTCC kk-d10-keke  83 3058
    1013932 N/A N/A 11119 11134 AGCAGTGATGTCAGGT kk-d10-keke  36 2718
    1013933 N/A N/A 11120 11135 AAGCAGTGATGTCAGG kk-d10-keke  24 3277
    1013934 N/A N/A 11121 11136 CAAGCAGTGATGTCAG kk-d10-keke  74 3278
    1013939 N/A N/A 11395 11410 CACATCAATGTTTTAG kk-d10-keke  61 3279
    1013940 N/A N/A 11396 11411 GCACATCAATGTTTTA kk-d10-keke  50 1159
    1013941 N/A N/A 11397 11412 GGCACATCAATGTTTT kk-d10-keke  91 3280
    1013942 N/A N/A 11398 11413 AGGCACATCAATGTTT kk-d10-keke  86 1233
    1013953 N/A N/A 11411 11426 GTGTATTACTCTTAGG kk-d10-keke  28 1540
    1013954 N/A N/A 11412 11427 TGTGTATTACTCTTAG kk-d10-keke  61 3246
    1013955 N/A N/A 11413 11428 ATGTGTATTACTCTTA kk-d10-keke  52 3281
    1013956 N/A N/A 11414 11429 AATGTGTATTACTCTT kk-d10-keke  78 3282
    1013969 N/A N/A 11565 11580 TGTGCTTGCCAAGCCT kk-d10-keke  70 3283
    1013970 N/A N/A 11566 11581 GTGTGCTTGCCAAGCC kk-d10-keke  53 3000
    1013971 N/A N/A 11567 11582 CGTGTGCTTGCCAAGC kk-d10-keke  55 3284
    1013972 N/A N/A 11568 11583 ACGTGTGCTTGCCAAG kk-d10-keke  74 3285
    1014004 N/A N/A 12514 12529 TTCATGTAAAGTCTGC kk-d10-keke  72 3286
    1014005 N/A N/A 12515 12530 GTTCATGTAAAGTCTG kk-d10-keke  58  934
    1014006 N/A N/A 12516 12531 AGTTCATGTAAAGTCT kk-d10-keke  51  755
    1014007 N/A N/A 12517 12532 AAGTTCATGTAAAGTC kk-d10-keke  80 3287
    1014086 N/A N/A 18073 18088 GTTGGCTGGTCTTTGT kk-d10-keke  75 3336
    1014087 N/A N/A 18074 18089 GGTTGGCTGGTCTTTG kk-d10-keke  24 3337
    1014088 N/A N/A 18075 18090 TGGTTGGCTGGTCTTT kk-d10-keke  20 3338
    1014089 N/A N/A 18076 18091 TTGGTTGGCTGGTCTT kk-d10-keke  73 3339
    1014092 N/A N/A 18087 18102 TTATATACTGGTTGGT kk-d10-keke  53 1179
    1014093 N/A N/A 18088 18103 ATTATATACTGGTTGG kk-d10-keke  68 3340
    1014094 N/A N/A 18089 18104 GATTATATACTGGTTG kk-d10-keke  55 1254
    1014095 N/A N/A 18090 18105 GGATTATATACTGGTT kk-d10-keke  22 1330
    1014096 N/A N/A 18091 18106 GGGATTATATACTGGT kk-d10-keke  54 3341
    1014097 N/A N/A 18092 18107 TGGGATTATATACTGG kk-d10-keke  32 3342
    1014111 N/A N/A 18571 18586 TGATAGCTGAGCTGAT kk-d10-keke 117 2546
    1014112 N/A N/A 18572 18587 GTGATAGCTGAGCTGA kk-d10-keke  65 3343
    1014113 N/A N/A 18573 18588 TGTGATAGCTGAGCTG kk-d10-keke  84 3344
    1014114 N/A N/A 18574 18589 ATGTGATAGCTGAGCT kk-d10-keke  96 3345
    1014115 N/A N/A 18575 18590 GATGTGATAGCTGAGC kk-d10-keke  36 3346
    1014116 N/A N/A 18576 18591 TGATGTGATAGCTGAG kk-d10-keke  46 3347
    1014117 N/A N/A 18577 18592 TTGATGTGATAGCTGA kk-d10-keke  89 3348
  • TABLE 61
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence Motif (% UTC) ID NO
     609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT kkk-d10-kkk  24  195
     881450 3252 3267 21369 21384 ACACTTTTAGAGAGGA kkk-d10-kkk  32 2111
     881659 4592 4607 22709 22724 GGAAGTTTACACTGGA kkk-d10-kkk  11 2044
    1014131 N/A N/A 18611 18626 AGTGACTTGCATCCAT kk-d10-keke  50 3349
    1014132 N/A N/A 18612 18627 CAGTGACTTGCATCCA kk-d10-keke  67 3350
    1014133 N/A N/A 18613 18628 ACAGTGACTTGCATCC kk-d10-keke  70 3351
    1014134 N/A N/A 18614 18629 GACAGTGACTTGCATC kk-d10-keke  75 3352
    1014342 N/A N/A 10142 10157 ATGTTAGCCAATTCCT kk-d9-kdkdk  97 3272
    1014343 N/A N/A 10143 10158 TATGTTAGCCAATTCC kk-d9-kdkdk  66 2991
    1014344 N/A N/A 10144 10159 TTATGTTAGCCAATTC kk-d9-kdkdk  74 3273
    1014345 N/A N/A 10145 10160 TTTATGTTAGCCAATT kk-d9-kdkdk  66 3274
    1014351 N/A N/A 10278 10293 TGTTACCGATGCTTCA kk-d9-kdkdk  74 2294
    1014352 N/A N/A 10279 10294 CTGTTACCGATGCTTC kk-d9-kdkdk  48 2993
    1014353 N/A N/A 10280 10295 ACTGTTACCGATGCTT kk-d9-kdkdk  69 3055
    1014354 N/A N/A 10281 10296 TACTGTTACCGATGCT kk-d9-kdkdk  82 3117
    1014365 N/A N/A 11016 11031 GTGTCTAAAGTCCCAT kk-d9-kdkdk  95 3275
    1014366 N/A N/A 11017 11032 AGTGTCTAAAGTCCCA kk-d9-kdkdk 105 2996
    1014367 N/A N/A 11018 11033 AAGTGTCTAAAGTCCC kk-d9-kdkdk  79 3276
    1014368 N/A N/A 11019 11034 CAAGTGTCTAAAGTCC kk-d9-kdkdk  71 3058
    1014372 N/A N/A 11119 11134 AGCAGTGATGTCAGGT kk-d9-kdkdk  52 2718
    1014373 N/A N/A 11120 11135 AAGCAGTGATGTCAGG kk-d9-kdkdk  39 3277
    1014374 N/A N/A 11121 11136 CAAGCAGTGATGTCAG kk-d9-kdkdk  51 3278
    1014379 N/A N/A 11395 11410 CACATCAATGTTTTAG kk-d9-kdkdk  63 3279
    1014380 N/A N/A 11396 11411 GCACATCAATGTTTTA kk-d9-kdkdk  93 1159
    1014381 N/A N/A 11397 11412 GGCACATCAATGTTTT kk-d9-kdkdk  84 3280
    1014382 N/A N/A 11398 11413 AGGCACATCAATGTTT kk-d9-kdkdk  81 1233
    1014393 N/A N/A 11411 11426 GTGTATTACTCTTAGG kk-d9-kdkdk  17 1540
    1014394 N/A N/A 11412 11427 TGTGTATTACTCTTAG kk-d9-kdkdk  29 3246
    1014395 N/A N/A 11413 11428 ATGTGTATTACTCTTA kk-d9-kdkdk  68 3281
    1014396 N/A N/A 11414 11429 AATGTGTATTACTCTT kk-d9-kdkdk  85 3282
    1014409 N/A N/A 11565 11580 TGTGCTTGCCAAGCCT kk-d9-kdkdk  79 3283
    1014410 N/A N/A 11566 11581 GTGTGCTTGCCAAGCC kk-d9-kdkdk  41 3000
    1014411 N/A N/A 11567 11582 CGTGTGCTTGCCAAGC kk-d9-kdkdk  47 3284
    1014412 N/A N/A 11568 11583 ACGTGTGCTTGCCAAG kk-d9-kdkdk  34 3285
    1014444 N/A N/A 12514 12529 TTCATGTAAAGTCTGC kk-d9-kdkdk  65 3286
    1014445 N/A N/A 12515 12530 GTTCATGTAAAGTCTG kk-d9-kdkdk  64  934
    1014446 N/A N/A 12516 12531 AGTTCATGTAAAGTCT kk-d9-kdkdk  53  755
    1014447 N/A N/A 12517 12532 AAGTTCATGTAAAGTC kk-d9-kdkdk  66 3287
    1014526 N/A N/A 18073 18088 GTTGGCTGGTCTTTGT kk-d9-kdkdk  44 3336
    1014527 N/A N/A 18074 18089 GGTTGGCTGGTCTTTG kk-d9-kdkdk  36 3337
    1014528 N/A N/A 18075 18090 TGGTTGGCTGGTCTTT kk-d9-kdkdk  49 3338
    1014529 N/A N/A 18076 18091 TTGGTTGGCTGGTCTT kk-d9-kdkdk  45 3339
    1014532 N/A N/A 18087 18102 TTATATACTGGTTGGT kk-d9-kdkdk  82 1179
    1014533 N/A N/A 18088 18103 ATTATATACTGGTTGG kk-d9-kdkdk  72 3340
    1014534 N/A N/A 18089 18104 GATTATATACTGGTTG kk-d9-kdkdk  65 1254
    1014535 N/A N/A 18090 18105 GGATTATATACTGGTT kk-d9-kdkdk  41 1330
    1014536 N/A N/A 18091 18106 GGGATTATATACTGGT kk-d9-kdkdk  59 3341
    1014537 N/A N/A 18092 18107 TGGGATTATATACTGG kk-d9-kdkdk  75 3342
    1014551 N/A N/A 18571 18586 TGATAGCTGAGCTGAT kk-d9-kdkdk 122 2546
    1014552 N/A N/A 18572 18587 GTGATAGCTGAGCTGA kk-d9-kdkdk  66 3343
    1014553 N/A N/A 18573 18588 TGTGATAGCTGAGCTG kk-d9-kdkdk  53 3344
    1014554 N/A N/A 18574 18589 ATGTGATAGCTGAGCT kk-d9-kdkdk  73 3345
    1014555 N/A N/A 18575 18590 GATGTGATAGCTGAGC kk-d9-kdkdk  66 3346
    1014556 N/A N/A 18576 18591 TGATGTGATAGCTGAG kk-d9-kdkdk  86 3347
    1014557 N/A N/A 18577 18592 TTGATGTGATAGCTGA kk-d9-kdkdk  64 3348
    1014571 N/A N/A 18611 18626 AGTGACTTGCATCCAT kk-d9-kdkdk  78 3349
    1014572 N/A N/A 18612 18627 CAGTGACTTGCATCCA kk-d9-kdkdk  64 3350
    1014573 N/A N/A 18613 18628 ACAGTGACTTGCATCC kk-d9-kdkdk  82 3351
    1014574 N/A N/A 18614 18629 GACAGTGACTTGCATC kk-d9-kdkdk 107 3352
    1014783 N/A N/A 10142 10157 ATGTTAGCCAATTCCT kk-d9-ecekk  94 3272
    1014784 N/A N/A 10143 10158 TATGTTAGCCAATTCC kk-d9-ecekk  73 2991
    1014785 N/A N/A 10144 10159 TTATGTTAGCCAATTC kk-d9-ecekk  91 3273
    1014786 N/A N/A 10145 10160 TTTATGTTAGCCAATT kk-d9-eeekk  79 3274
    1014792 N/A N/A 10278 10293 TGTTACCGATGCTTCA kk-d9-eeekk  61 2294
    1014793 N/A N/A 10279 10294 CTGTTACCGATGCTTC kk-d9-eeekk  44 2993
    1014794 N/A N/A 10280 10295 ACTGTTACCGATGCTT kk-d9-eeekk  66 3055
    1014795 N/A N/A 10281 10296 TACTGTTACCGATGCT kk-d9-eeekk  92 3117
    1014806 N/A N/A 11016 11031 GTGTCTAAAGTCCCAT kk-d9-eeekk 123 3275
    1014807 N/A N/A 11017 11032 AGTGTCTAAAGTCCCA kk-d9-eeekk  88 2996
    1014808 N/A N/A 11018 11033 AAGTGTCTAAAGTCCC kk-d9-eeekk  54 3276
    1014809 N/A N/A 11019 11034 CAAGTGTCTAAAGTCC kk-d9-eeekk  69 3058
    1014813 N/A N/A 11119 11134 AGCAGTGATGTCAGGT kk-d9-eeekk  44 2718
    1014814 N/A N/A 11120 11135 AAGCAGTGATGTCAGG kk-d9-eeekk  49 3277
    1014815 N/A N/A 11121 11136 CAAGCAGTGATGTCAG kk-d9-eeekk  92 3278
    1014820 N/A N/A 11395 11410 CACATCAATGTTTTAG kk-d9-eeekk  89 3279
    1014821 N/A N/A 11396 11411 GCACATCAATGTTTTA kk-d9-eeekk  80 1159
    1014822 N/A N/A 11397 11412 GGCACATCAATGTTTT kk-d9-eeekk  64 3280
    1014823 N/A N/A 11398 11413 AGGCACATCAATGTTT kk-d9-eeekk  57 1233
    1014834 N/A N/A 11411 11426 GTGTATTACTCTTAGG kk-d9-eeekk  25 1540
  • TABLE 62
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence Motif (% UTC) ID NO
    609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT kkk-d10-kkk  26  195
    881450 3252 3267 21369 21384 ACACTTTTAGAGAGGA kkk-d10-kkk  39 2111
    881659 4592 4607 22709 22724 GGAAGTTTACACTGGA kkk-d10-kkk   9 2044
    1014835 N/A N/A 11412 11427 TGTGTATTACTCTTAG kk-d9-eeekk  76 3246
    1014836 N/A N/A 11413 11428 ATGTGTATTACTCTTA kk-d9-eeekk  56 3281
    1014837 N/A N/A 11414 11429 AATGTGTATTACTCTT kk-d9-eeekk  83 3282
    1014850 N/A N/A 11565 11580 TGTGCTTGCCAAGCCT kk-d9-eeekk  60 3283
    1014851 N/A N/A 11566 11581 GTGTGCTTGCCAAGCC kk-d9-eeekk  38 3000
    1014852 N/A N/A 11567 11582 CGTGTGCTTGCCAAGC kk-d9-eeekk  34 3284
    1014853 N/A N/A 11568 11583 ACGTGTGCTTGCCAAG kk-d9-eeekk  57 3285
    1014885 N/A N/A 12514 12529 TTCATGTAAAGTCTGC kk-d9-eeekk  65 3286
    1014886 N/A N/A 12515 12530 GTTCATGTAAAGTCTG kk-d9-eeekk  76  934
    1014887 N/A N/A 12516 12531 AGTTCATGTAAAGTCT kk-d9-eeekk  70  755
    1014888 N/A N/A 12517 12532 AAGTTCATGTAAAGTC kk-d9-eeekk  97 3287
    1014967 N/A N/A 18073 18088 GTTGGCTGGTCTTTGT kk-d9-eeekk  76 3336
    1014968 N/A N/A 18074 18089 GGTTGGCTGGTCTTTG kk-d9-eeekk  31 3337
    1014969 N/A N/A 18075 18090 TGGTTGGCTGGTCTTT kk-d9-eeekk  60 3338
    1014970 N/A N/A 18076 18091 TTGGTTGGCTGGTCTT kk-d9-eeekk  50 3339
    1014973 N/A N/A 18087 18102 TTATATACTGGTTGGT kk-d9-eeekk  60 1179
    1014974 N/A N/A 18088 18103 ATTATATACTGGTTGG kk-d9-eeekk  63 3340
    1014975 N/A N/A 18089 18104 GATTATATACTGGTTG kk-d9-eeekk  58 1254
    1014976 N/A N/A 18090 18105 GGATTATATACTGGTT kk-d9-eeekk  22 1330
    1014977 N/A N/A 18091 18106 GGGATTATATACTGGT kk-d9-eeekk  65 3341
    1014978 N/A N/A 18092 18107 TGGGATTATATACTGG kk-d9-eeekk  46 3342
    1014992 N/A N/A 18571 18586 TGATAGCTGAGCTGAT kk-d9-eeekk 102 2546
    1014993 N/A N/A 18572 18587 GTGATAGCTGAGCTGA kk-d9-eeekk  87 3343
    1014994 N/A N/A 18573 18588 TGTGATAGCTGAGCTG kk-d9-eeekk  88 3344
    1014995 N/A N/A 18574 18589 ATGTGATAGCTGAGCT kk-d9-eeekk 100 3345
    1014996 N/A N/A 18575 18590 GATGTGATAGCTGAGC kk-d9-eeekk  48 3346
    1014997 N/A N/A 18576 18591 TGATGTGATAGCTGAG kk-d9-eeekk  53 3347
    1014998 N/A N/A 18577 18592 TTGATGTGATAGCTGA kk-d9-eeekk  83 3348
    1015012 N/A N/A 18611 18626 AGTGACTTGCATCCAT kk-d9-eeekk  48 3349
    1015013 N/A N/A 18612 18627 CAGTGACTTGCATCCA kk-d9-eeekk  72 3350
    1015014 N/A N/A 18613 18628 ACAGTGACTTGCATCC kk-d9-eeekk  73 3351
    1015015 N/A N/A 18614 18629 GACAGTGACTTGCATC kk-d9-eeekk  76 3352
    1015224 N/A N/A 10142 10157 ATGTTAGCCAATTCCT kk-d9-ekeke  70 3272
    1015225 N/A N/A 10143 10158 TATGTTAGCCAATTCC kk-d9-ekeke 110 2991
    1015226 N/A N/A 10144 10159 TTATGTTAGCCAATTC kk-d9-ekeke  92 3273
    1015227 N/A N/A 10145 10160 TTTATGTTAGCCAATT kk-d9-ekeke 113 3274
    1015233 N/A N/A 10278 10293 TGTTACCGATGCTTCA kk-d9-ekeke  51 2294
    1015234 N/A N/A 10279 10294 CTGTTACCGATGCTTC kk-d9-ekeke  40 2993
    1015235 N/A N/A 10280 10295 ACTGTTACCGATGCTT kk-d9-ekeke  63 3055
    1015236 N/A N/A 10281 10296 TACTGTTACCGATGCT kk-d9-ekeke  86 3117
    1015247 N/A N/A 11016 11031 GTGTCTAAAGTCCCAT kk-d9-ekeke  77 3275
    1015248 N/A N/A 11017 11032 AGTGTCTAAAGTCCCA kk-d9-ekeke  81 2996
    1015249 N/A N/A 11018 11033 AAGTGTCTAAAGTCCC kk-d9-ekeke 101 3276
    1015250 N/A N/A 11019 11034 CAAGTGTCTAAAGTCC kk-d9-ekeke  75 3058
    1015254 N/A N/A 11119 11134 AGCAGTGATGTCAGGT kk-d9-ekeke  30 2718
    1015255 N/A N/A 11120 11135 AAGCAGTGATGTCAGG kk-d9-ekeke  35 3277
    1015256 N/A N/A 11121 11136 CAAGCAGTGATGTCAG kk-d9-ekeke  66 3278
    1015261 N/A N/A 11395 11410 CACATCAATGTTTTAG kk-d9-ekeke  73 3279
    1015262 N/A N/A 11396 11411 GCACATCAATGTTTTA kk-d9-ekeke  88 1159
    1015263 N/A N/A 11397 11412 GGCACATCAATGTTTT kk-d9-ekeke  74 3280
    1015264 N/A N/A 11398 11413 AGGCACATCAATGTTT kk-d9-ekeke  65 1233
    1015275 N/A N/A 11411 11426 GTGTATTACTCTTAGG kk-d9-ekeke  16 1540
    1015276 N/A N/A 11412 11427 TGTGTATTACTCTTAG kk-d9-ekeke  34 3246
    1015277 N/A N/A 11413 11428 ATGTGTATTACTCTTA kk-d9-ekeke  39 3281
    1015278 N/A N/A 11414 11429 AATGTGTATTACTCTT kk-d9-ekeke  70 3282
    1015291 N/A N/A 11565 11580 TGTGCTTGCCAAGCCT kk-d9-ekeke  99 3283
    1015292 N/A N/A 11566 11581 GTGTGCTTGCCAAGCC kk-d9-ekeke  81 3000
    1015293 N/A N/A 11567 11582 CGTGTGCTTGCCAAGC kk-d9-ekeke  64 3284
    1015294 N/A N/A 11568 11583 ACGTGTGCTTGCCAAG kk-d9-ekeke  39 3285
    1015326 N/A N/A 12514 12529 TTCATGTAAAGTCTGC kk-d9-ekeke  61 3286
    1015327 N/A N/A 12515 12530 GTTCATGTAAAGTCTG kk-d9-ekeke  68  934
    1015328 N/A N/A 12516 12531 AGTTCATGTAAAGTCT kk-d9-ekeke  51  755
    1015329 N/A N/A 12517 12532 AAGTTCATGTAAAGTC kk-d9-ekeke  71 3287
    1015408 N/A N/A 18073 18088 GTTGGCTGGTCTTTGT kk-d9-ekeke  77 3336
    1015409 N/A N/A 18074 18089 GGTTGGCTGGTCTTTG kk-d9-ekeke  27 3337
    1015410 N/A N/A 18075 18090 TGGTTGGCTGGTCTTT kk-d9-ekeke  40 3338
    1015411 N/A N/A 18076 18091 TTGGTTGGCTGGTCTT kk-d9-ekeke  66 3339
    1015414 N/A N/A 18087 18102 TTATATACTGGTTGGT kk-d9-ekeke  36 1179
    1015415 N/A N/A 18088 18103 ATTATATACTGGTTGG kk-d9-ekeke  57 3340
    1015416 N/A N/A 18089 18104 GATTATATACTGGTTG kk-d9-ekeke  54 1254
    1015417 N/A N/A 18090 18105 GGATTATATACTGGTT kk-d9-ekeke  21 1330
    1015418 N/A N/A 18091 18106 GGGATTATATACTGGT kk-d9-ekeke  66 3341
    1015419 N/A N/A 18092 18107 TGGGATTATATACTGG kk-d9-ekeke  37 3342
    1015433 N/A N/A 18571 18586 TGATAGCTGAGCTGAT kk-d9-ekeke  85 2546
    1015434 N/A N/A 18572 18587 GTGATAGCTGAGCTGA kk-d9-ekeke  76 3343
    1015435 N/A N/A 18573 18588 TGTGATAGCTGAGCTG kk-d9-ekeke  59 3344
  • TABLE 63
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence Motif (% UTC) ID NO
     609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT kkk-d10-kkk  33  195
     881450 3252 3267 21369 21384 ACACTTTTAGAGAGGA kkk-d10-kkk  30 2111
     881659 4592 4607 22709 22724 GGAAGTTTACACTGGA kkk-d10-kkk  13 2044
    1012810 N/A N/A 10142 10157 ATGTTAGCCAATTCCT kkk-d10-kkk  67 3272
    1012811 N/A N/A 10144 10159 TTATGTTAGCCAATTC kkk-d10-kkk  78 3273
    1012812 N/A N/A 10145 10160 TTTATGTTAGCCAATT kkk-d10-kkk  87 3274
    1012816 N/A N/A 11016 11031 GTGTCTAAAGTCCCAT kkk-d10-kkk  72 3275
    1012817 N/A N/A 11018 11033 AAGTGTCTAAAGTCCC kkk-d10-kkk  59 3276
    1012819 N/A N/A 11120 11135 AAGCAGTGATGTCAGG kkk-d10-kkk  34 3277
    1012820 N/A N/A 11121 11136 CAAGCAGTGATGTCAG kkk-d10-kkk  49 3278
    1012821 N/A N/A 11395 11410 CACATCAATGTTTTAG kkk-d10-kkk  25 3279
    1012822 N/A N/A 11397 11412 GGCACATCAATGTTTT kkk-d10-kkk  86 3280
    1012826 N/A N/A 11413 11428 ATGTGTATTACTCTTA kkk-d10-kkk  51 3281
    1012827 N/A N/A 11414 11429 AATGTGTATTACTCTT kkk-d10-kkk  59 3282
    1012835 N/A N/A 11565 11580 TGTGCTTGCCAAGCCT kkk-d10-kkk  51 3283
    1012836 N/A N/A 11567 11582 CGTGTGCTTGCCAAGC kkk-d10-kkk  34 3284
    1012837 N/A N/A 11568 11583 ACGTGTGCTTGCCAAG kkk-d10-kkk  45 3285
    1012845 N/A N/A 12514 12529 TTCATGTAAAGTCTGC kkk-d10-kkk  45 3286
    1012846 N/A N/A 12517 12532 AAGTTCATGTAAAGTC kkk-d10-kkk  59 3287
    1015436 N/A N/A 18574 18589 ATGTGATAGCTGAGCT kk-d9-ekeke  98 3345
    1015437 N/A N/A 18575 18590 GATGTGATAGCTGAGC kk-d9-ekeke  47 3346
    1015438 N/A N/A 18576 18591 TGATGTGATAGCTGAG kk-d9-ekeke  40 3347
    1015439 N/A N/A 18577 18592 TTGATGTGATAGCTGA kk-d9-ekeke  72 3348
    1015453 N/A N/A 18611 18626 AGTGACTTGCATCCAT kk-d9-ekeke  66 3349
    1015454 N/A N/A 18612 18627 CAGTGACTTGCATCCA kk-d9-ekeke  66 3350
    1015455 N/A N/A 18613 18628 ACAGTGACTTGCATCC kk-d9-ekeke  91 3351
    1015456 N/A N/A 18614 18629 GACAGTGACTTGCATC kk-d9-ekeke  70 3352
    1015665 N/A N/A 10142 10157 ATGTTAGCCAATTCCT k-d9-kekeke  95 3272
    1015666 N/A N/A 10143 10158 TATGTTAGCCAATTCC k-d9-kekeke  86 2991
    1015667 N/A N/A 10144 10159 TTATGTTAGCCAATTC k-d9-kekeke  98 3273
    1015668 N/A N/A 10145 10160 TTTATGTTAGCCAATT k-d9-kekeke  86 3274
    1015674 N/A N/A 10278 10293 TGTTACCGATGCTTCA k-d9-kekeke  87 2294
    1015675 N/A N/A 10279 10294 CTGTTACCGATGCTTC k-d9-kekeke  76 2993
    1015676 N/A N/A 10280 10295 ACTGTTACCGATGCTT k-d9-kekeke  83 3055
    1015677 N/A N/A 10281 10296 TACTGTTACCGATGCT k-d9-kekeke  82 3117
    1015688 N/A N/A 11016 11031 GTGTCTAAAGTCCCAT k-d9-kekeke  95 3275
    1015689 N/A N/A 11017 11032 AGTGTCTAAAGTCCCA k-d9-kekeke  88 2996
    1015690 N/A N/A 11018 11033 AAGTGTCTAAAGTCCC k-d9-kekeke  95 3276
    1015691 N/A N/A 11019 11034 CAAGTGTCTAAAGTCC k-d9-kekeke  90 3058
    1015695 N/A N/A 11119 11134 AGCAGTGATGTCAGGT k-d9-kekeke  64 2718
    1015696 N/A N/A 11120 11135 AAGCAGTGATGTCAGG k-d9-kekeke  65 3277
    1015697 N/A N/A 11121 11136 CAAGCAGTGATGTCAG k-d9-kekeke  88 3278
    1015702 N/A N/A 11395 11410 CACATCAATGTTTTAG k-d9-kekeke  82 3279
    1015703 N/A N/A 11396 11411 GCACATCAATGTTTTA k-d9-kekeke  85 1159
    1015704 N/A N/A 11397 11412 GGCACATCAATGTTTT k-d9-kekeke  94 3280
    1015705 N/A N/A 11398 11413 AGGCACATCAATGTTT k-d9-kekeke  97 1233
    1015716 N/A N/A 11411 11426 GTGTATTACTCTTAGG k-d9-kekeke  23 1540
    1015717 N/A N/A 11412 11427 TGTGTATTACTCTTAG k-d9-kekeke  48 3246
    1015718 N/A N/A 11413 11428 ATGTGTATTACTCTTA k-d9-kekeke  51 3281
    1015719 N/A N/A 11414 11429 AATGTGTATTACTCTT k-d9-kekeke  85 3282
    1015732 N/A N/A 11565 11580 TGTGCTTGCCAAGCCT k-d9-kekeke  84 3283
    1015733 N/A N/A 11566 11581 GTGTGCTTGCCAAGCC k-d9-kekeke  78 3000
    1015734 N/A N/A 11567 11582 CGTGTGCTTGCCAAGC k-d9-kekeke  89 3284
    1015735 N/A N/A 11568 11583 ACGTGTGCTTGCCAAG k-d9-kekeke  65 3285
    1015767 N/A N/A 12514 12529 TTCATGTAAAGTCTGC k-d9-kekeke  97 3286
    1015768 N/A N/A 12515 12530 GTTCATGTAAAGTCTG k-d9-kekeke  90  934
    1015769 N/A N/A 12516 12531 AGTTCATGTAAAGTCT k-d9-kekeke  90  755
    1015770 N/A N/A 12517 12532 AAGTTCATGTAAAGTC k-d9-kekeke  79 3287
    1015849 N/A N/A 18073 18088 GTTGGCTGGTCTTTGT k-d9-kekeke  82 3336
    1015850 N/A N/A 18074 18089 GGTTGGCTGGTCTTTG k-d9-kekeke  74 3337
    1015851 N/A N/A 18075 18090 TGGTTGGCTGGTCTTT k-d9-kekeke  69 3338
    1015852 N/A N/A 18076 18091 TTGGTTGGCTGGTCTT k-d9-kekeke 107 3339
    1015855 N/A N/A 18087 18102 TTATATACTGGTTGGT k-d9-kekeke  80 1179
    1015856 N/A N/A 18088 18103 ATTATATACTGGTTGG k-d9-kekeke  73 3340
    1015857 N/A N/A 18089 18104 GATTATATACTGGTTG k-d9-kekeke  88 1254
    1015858 N/A N/A 18090 18105 GGATTATATACTGGTT k-d9-kekeke  90 1330
    1015859 N/A N/A 18091 18106 GGGATTATATACTGGT k-d9-kekeke  71 3341
    1015860 N/A N/A 18092 18107 TGGGATTATATACTGG k-d9-kekeke  60 3342
    1015874 N/A N/A 18571 18586 TGATAGCTGAGCTGAT k-d9-kekeke  83 2546
    1015875 N/A N/A 18572 18587 GTGATAGCTGAGCTGA k-d9-kekeke  84 3343
    1015876 N/A N/A 18573 18588 TGTGATAGCTGAGCTG k-d9-kekeke  82 3344
    1015877 N/A N/A 18574 18589 ATGTGATAGCTGAGCT k-d9-kekeke  85 3345
    1015878 N/A N/A 18575 18590 GATGTGATAGCTGAGC k-d9-kekeke  82 3346
    1015879 N/A N/A 18576 18591 TGATGTGATAGCTGAG k-d9-kekeke  53 3347
    1015880 N/A N/A 18577 18592 TTGATGTGATAGCTGA k-d9-kekeke  66 3348
    1015894 N/A N/A 18611 18626 AGTGACTTGCATCCAT k-d9-kekeke  92 3349
    1015895 N/A N/A 18612 18627 CAGTGACTTGCATCCA k-d9-kekeke  81 3350
    1015896 N/A N/A 18613 18628 ACAGTGACTTGCATCC k-d9-kekeke  94 3351
    1015897 N/A N/A 18614 18629 GACAGTGACTTGCATC k-d9-kekeke 100 3352
  • TABLE 64
    Percent control of human IRF4 mRNA with gapmers
    with phosphorothioate internucleoside linkages
    SEQ ID: 1 SEQ ID: 1 SEQ ID: 2 SEQ ID: 2
    Compound Start Stop Start Stop IRF4 SEQ
    Number Site Site Site Site Sequence Motif (% UTC) ID NO
     609408 4226 4241 22343 22358 TTGTAAATGAGTCGGT kkk-d10-kkk 23  195
     881450 3252 3267 21369 21384 ACACTTTTAGAGAGGA kkk-d10-kkk 35 2111
     881659 4592 4607 22709 22724 GGAAGTTTACACTGGA kkk-d10-kkk  9 2044
     935595 3075 3090 21192 21207 ACTAAGCTTGATAAAG kkk-d10-kkk 95 3288
     935607 4195 4210 22312 22327 AGTGTTCCAGGAGATA kkk-d10-kkk 28 3289
    1012769 N/A N/A  4810  4825 GCTCCCGACACGCGCC kkk-d10-kkk 81 3290
    1012772 N/A N/A  6267  6282 ATGCGGAGGTTCCTTG kkk-d10-kkk 48 3291
    1012774 N/A N/A  6271  6286 TGAGATGCGGAGGTTC kkk-d10-kkk 73 3292
    1012775 N/A N/A  6273  6288 AGTGAGATGCGGAGGT kkk-d10-kkk 35 3293
    1012776 N/A N/A  6275  6290 AGAGTGAGATGCGGAG kkk-d10-kkk 37 3294
    1012778 N/A N/A  6281  6296 ACCGGTAGAGTGAGAT kkk-d10-kkk 98 3295
    1012782 N/A N/A  7634  7649 GAGTTGTACAGGACAG kkk-d10-kkk 48 3296
    1012785 N/A N/A  7638  7653 GTCTGAGTTGTACAGG kkk-d10-kkk 43 3297
    1012786 N/A N/A  7640  7655 AGGTCTGAGTTGTACA kkk-d10-kkk 55 3298
    1012788 N/A N/A  8386  8401 AATGGAGATACTTGTA kkk-d10-kkk 74 3299
    1012790 N/A N/A  8389  8404 GACAATGGAGATACTT kkk-d10-kkk 63 3300
    1012795 N/A N/A  9667  9682 GTATTTTTCCGTTCCT kkk-d10-kkk 16 3303
    1012796 N/A N/A  9670  9685 ATGGTATTTTTCCGTT kkk-d10-kkk 57 3304
    1012799 N/A N/A  9677  9692 GTTTGCCATGGTATTT kkk-d10-kkk 50 3305
    1012804 N/A N/A  9840  9855 CATTGCTAGATTCTCC kkk-d10-kkk 70 3306
    1012806 N/A N/A  9846  9861 TTACCGCATTGCTAGA kkk-d10-kkk 74 3307
    1012808 N/A N/A  9851  9866 CTGAGTTACCGCATTG kkk-d10-kkk 46 3308
    1012809 N/A N/A 10139 10154 TTAGCCAATTCCTCCA kkk-d10-kkk 53 3309
    1012813 N/A N/A 10274 10289 ACCGATGCTTCAAGAC kkk-d10-kkk 44 3310
    1012814 N/A N/A 10276 10291 TTACCGATGCTTCAAG kkk-d10-kkk 81 3311
    1012815 N/A N/A 10282 10297 TTACTGTTACCGATGC kkk-d10-kkk 65 3312
    1012818 N/A N/A 11020 11035 GCAAGTGTCTAAAGTC kkk-d10-kkk 47 3313
    1012823 N/A N/A 11400 11415 TTAGGCACATCAATGT kkk-d10-kkk 83 3314
    1012825 N/A N/A 11406 11421 TTACTCTTAGGCACAT kkk-d10-kkk 55 3315
    1012828 N/A N/A 11523 11538 GATCTCCATGGTGCAG kkk-d10-kkk 88 3316
    1012831 N/A N/A 11530 11545 TAGGTAAGATCTCCAT kkk-d10-kkk 67 3317
    1012834 N/A N/A 11564 11579 GTGCTTGCCAAGCCTA kkk-d10-kkk 64 3318
    1012840 N/A N/A 11659 11674 CCAAACCTTAAGCTAT kkk-d10-kkk 66 3319
    1012841 N/A N/A 11663 11678 AATTCCAAACCTTAAG kkk-d10-kkk 74 3320
    1012843 N/A N/A 11995 12010 AGGTTGCCGAGATATA kkk-d10-kkk 33 3321
    1012844 N/A N/A 11997 12012 CGAGGTTGCCGAGATA kkk-d10-kkk 40 3322
    1012848 N/A N/A 14251 14266 GAGCCAACTTATAGCA kkk-d10-kkk 92 3323
    1012850 N/A N/A 14253 14268 CAGAGCCAACTTATAG kkk-d10-kkk 57 3324
    1012852 N/A N/A 14734 14749 GAAGCTTAGTTATCTG kkk-d10-kkk 61 3325
    1012855 N/A N/A 14739 14754 GGCCTGAAGCTTAGTT kkk-d10-kkk 94 3326
    1012859 N/A N/A 15594 15609 GTCGCGCAAGTCTACA kkk-d10-kkk 84 3327
    1012860 N/A N/A 15841 15856 GTTGGCACAATTCTCT kkk-d10-kkk 84 3328
    1012864 N/A N/A 15845 15860 GCGAGTTGGCACAATT kkk-d10-kkk 63 3329
    1012866 N/A N/A 15848 15863 ATGGCGAGTTGGCACA kkk-d10-kkk 52 3330
    1012867 N/A N/A 15850 15865 GAATGGCGAGTTGGCA kkk-d10-kkk 60 3331
    1012869 N/A N/A 15884 15899 CGTGATCTGAGACTAC kkk-d10-kkk 64 3332
    1012872 N/A N/A 15889 15904 ACTGCCGTGATCTGAG kkk-d10-kkk 71 3333
    1012875 N/A N/A 17236 17251 TTACGCTTATTTTTCC kkk-d10-kkk 61 3353
    1012879 N/A N/A 17473 17488 CAATCTTAACCTGGAG kkk-d10-kkk 60 3354
    1012881 N/A N/A 18073 18088 GTTGGCTGGTCTTTGT kkk-d10-kkk 37 3336
    1012882 N/A N/A 18075 18090 TGGTTGGCTGGTCTTT kkk-d10-kkk 12 3338
    1012883 N/A N/A 18076 18091 TTGGTTGGCTGGTCTT kkk-d10-kkk 24 3339
    1012884 N/A N/A 18083 18098 ATACTGGTTGGTTGGC kkk-d10-kkk 31 3355
    1012885 N/A N/A 18250 18265 GCCGATCATCAACTTC kkk-d10-kkk 74 3356
    1012888 N/A N/A 18254 18269 CCCGGCCGATCATCAA kkk-d10-kkk 77 3357
    1012889 N/A N/A 18569 18584 ATAGCTGAGCTGATCA kkk-d10-kkk 70 3358
    1012890 N/A N/A 18573 18588 TGTGATAGCTGAGCTG kkk-d10-kkk 53 3344
    1012891 N/A N/A 18574 18589 ATGTGATAGCTGAGCT kkk-d10-kkk 74 3345
    1012892 N/A N/A 18576 18591 TGATGTGATAGCTGAG kkk-d10-kkk 41 3347
    1012893 N/A N/A 18577 18592 TTGATGTGATAGCTGA kkk-d10-kkk 45 3348
    1012895 N/A N/A 18581 18596 TGGATTGATGTGATAG kkk-d10-kkk 52 3359
    1012897 N/A N/A 18607 18622 ACTTGCATCCATGTCA kkk-d10-kkk 65 3360
    1012899 N/A N/A 18610 18625 GTGACTTGCATCCATG kkk-d10-kkk 38 3361
    1012900 N/A N/A 18611 18626 AGTGACTTGCATCCAT kkk-d10-kkk 33 3349
    1012901 N/A N/A 18613 18628 ACAGTGACTTGCATCC kkk-d10-kkk 66 3351
    1012902 N/A N/A 18614 18629 GACAGTGACTTGCATC kkk-d10-kkk 76 3352
    1012903 N/A N/A 18722 18737 AAGTGGAACTCATAGG kkk-d10-kkk 75 3362
    1012904 N/A N/A 19021 19036 ATCTGTATAGTTCTCA kkk-d10-kkk 45 3363
    1012906 N/A N/A 19023 19038 TAATCTGTATAGTTCT kkk-d10-kkk 58 3364
    1012907 1344 1359 19461 19476 TCTGGCTAGCAGAGGT kkk-d10-kkk 74 3365
    1012911 1412 1427 19529 19544 ATGTGTTCTGGTAAAT kkk-d10-kkk 66 3366
    1012914 1422 1437 19539 19554 TGGATTGCTGATGTGT kkk-d10-kkk 29 3367
    1012915 1424 1439 19541 19556 TCTGGATTGCTGATGT kkk-d10-kkk 64 3368
    1012918 1427 1442 19544 19559 TCTTCTGGATTGCTGA kkk-d10-kkk 80 3369
    1012919 1429 1444 19546 19561 AATCTTCTGGATTGCT kkk-d10-kkk 86 3370
    1012920 1441 1456 19558 19573 TAGATCTGTGGTAATC kkk-d10-kkk 94 3334
    1012921 1450 1465 19567 19582 AATGGCGGATAGATCT kkk-d10-kkk 75 3335
  • Example 12: Effect of Modified Oligonucleotides on Human IRF4 In Vitro, Multiple Doses
  • Modified oligonucleotides selected from the examples above were tested at various doses in SK-MEL-28 cells. Cells were plated at a density of 20,000 cells per well and transfected using electroporation with 185 nM, 555 nM, 1,666 nM, 5,000 nM, and 15,000 nM concentrations of modified oligonucleotide, as specified in the tables below. After a treatment period of approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR. Human IRF4 primer probe set RTS3114 (described hereinabove in Example 1) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen. Results are presented as the percent level of IRF4 mRNA transcript, relative to that of untreated control (UTC) cells. As illustrated in the tables below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • TABLE 65
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% LTC)
    Number 185 nM 555 nM 1,666 nM 5,000 nM 15,000 nM
    609311 91 79 68 36 9
    609312 93 91 78 42 13
    609328 99 73 57 37 14
    609332 99 92 62 38 15
    609333 90 82 59 32 11
    609334 80 71 50 30 11
    609337 84 81 57 40 15
    609343 87 80 56 26 11
    609354 87 79 46 25 10
    609357 85 80 50 29 9
    609391 94 82 53 28 10
    609398 81 77 39 24 8
    609407 80 71 40 25 11
    609408 102 73 49 19 12
  • TABLE 66
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 185 nM 555 nM 1,666 nM 5,000 nM 15,000 nM
    609394 94 82 59 52 22
    609397 86 77 57 42 24
    609405 84 86 75 40 36
    609408 100 92 62 33 27
    609416 89 80 54 43 17
    609419 84 75 66 44 19
    609422 104 87 69 50 14
    609530 96 99 78 71 49
    609533 96 91 80 55 37
    609546 96 107 84 66 25
    609571 94 86 78 58 38
    609591 102 95 94 50 19
    609592 98 89 67 43 31
    609594 86 73 68 43 26
  • TABLE 67
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 185 nM 555 nM 1,666 nM 5,000 nM 15,000 nM
    609394 95 76 60 52 20
    609397 90 74 59 45 22
    609405 96 82 77 46 37
    609408 99 84 62 39 27
    609416 95 76 51 39 21
    609419 96 73 71 41 18
    609422 90 83 82 48 17
    609530 104 99 81 74 45
    609533 91 97 79 58 32
    609546 91 88 85 63 28
    609571 96 95 78 56 35
    609591 110 83 76 49 21
    609592 94 88 73 43 38
    609594 87 84 68 45 28
  • TABLE 68
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 185 nM 555 nM 1,666 nM 5,000 nM 15,000 nM
    609394 101 94 61 25 6
    609397 99 75 46 23 13
    609405 97 80 53 17 4
    609408 87 88 39 15 5
    609416 99 83 47 18 6
    609419 88 84 54 23 9
    609422 111 92 66 17 2
    609530 100 92 63 37 17
    609533 92 84 65 38 19
    609546 83 97 72 50 11
    609571 94 90 72 47 17
    609591 103 88 53 24 9
    609592 90 90 55 24 8
    609594 82 75 52 33 28
  • Example 13: Effect of Modified Oligonucleotides on Human IRF4 In Vitro, Multiple Doses
  • Modified oligonucleotides selected from the examples above were tested at various doses in SK-MEL-28 cells. Cells were plated at a density of 20,000 cells per well and transfected using electroporation with 500 nM, 1,000 nM, 2,000 nM, 4,000 nM, and 8,000 nM concentrations of modified oligonucleotide, as specified in the tables below. After a treatment period of approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR. Human IRF4 primer probe set RTS3114 (described hereinabove in Example 1) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen. Results are presented as the percent level of IRF4 mRNA transcript, relative to that of untreated control (UTC) cells. As illustrated in the tables below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • TABLE 69
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 500 nM 1,000 nM 2,000 nM 4,000 nM 8,000 nM
    609408 70 52 46 26 29
    666273 85 97 76 53 27
    666333 77 78 64 42 24
    666347 80 74 56 37 19
    666351 79 68 59 53 24
    666378 71 57 43 28 20
    666392 77 64 42 37 34
    666431 85 69 47 41 24
    666440 69 55 38 21 27
    666441 79 60 47 29 26
    666442 62 50 35 21 19
    666443 71 62 46 32 13
    666449 53 47 31 20 19
    666458 69 52 41 22 25
    666471 57 50 23 23 11
  • TABLE 70
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 500 nM 1,000 nM 2,000 nM 4,000 nM 8,000 nM
    609408 71 58 47 37 19
    666475 54 42 26 22 32
    666496 54 45 30 18 13
    666512 76 70 49 29 36
    666534 64 55 33 19 9
    666575 71 53 31 24 34
    666582 80 58 45 28 30
    666584 88 63 58 35 21
    666586 49 28 29 19 21
    666587 61 44 26 14 19
    666605 68 55 38 32 18
    666625 71 63 45 30 17
    666640 73 59 39 42 18
    666645 83 64 55 37 34
    666649 80 55 48 35 21
  • TABLE 71
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 500 nM 1,000 nM 2,000 nM 4,000 nM 8,000 nM
    609408 74 57 65 47 23
    666663 78 78 43 34 67
    666664 77 64 43 31 62
    666678 57 42 23 25 59
    666681 74 59 47 28 60
    666683 64 47 35 38 55
    666714 81 77 54 47 75
    666726 75 60 33 28 56
    666727 83 65 42 31 72
    666769 98 94 94 87 71
    666773 83 81 71 47 36
    666782 78 79 49 44 23
    666787 75 66 44 32 26
    666792 84 75 61 46 32
    666815 81 80 47 50 32
  • Example 14: Effect of Modified Oligonucleotides on Human IRF4 In Vitro, Multiple Doses
  • Modified oligonucleotides selected from the examples above were tested at various doses in SK-MEL-28 cells. Cells were plated at a density of 20,000 cells per well and transfected using electroporation with 296 nM, 888 nM, 2,666 nM, and 8,000 nM concentrations of modified oligonucleotide, as specified in the tables below. After a treatment period of approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR. Human IRF4 primer probe set RTS3114 (described hereinabove in Example 1) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen. Results are presented as the percent level of IRF4 mRNA transcript, relative to that of untreated control (UTC) cells. As illustrated in the tables below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • TABLE 72
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC) IC50
    Number 296 nM 888 nM 2,666 nM 8,000 nM (μM)
    609408 96 53 25 9 1.3
    881193 90 72 54 23 2.5
    881218 86 70 44 38 2.9
    881242 106 65 38 27 2.2
    881290 77 56 44 27 1.6
    881385 99 106 84 54 >8.0
    881409 91 82 51 28 2.9
    881434 78 59 29 14 1.2
    881506 61 37 15 11 0.5
    881667 80 63 41 16 1.5
    881993 94 101 73 43 >8.0
    882066 99 72 53 25 2.7
    882325 76 55 36 31 1.5
    882326 79 73 42 31 2.3
    882398 83 56 32 16 1.3
    882699 88 81 65 50 >8.0
    882722 97 102 84 58 >8.0
    882818 134 94 75 31 4.8
    882898 80 66 48 26 2.1
  • TABLE 73
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC) IC50
    Number 296 nM 888 nM 2,666 nM 8,000 nM (μM)
    609408 85 50 22 11 1.1
    881411 101 70 45 22 2.3
    881412 105 74 33 21 2.1
    881460 71 50 26 17 0.9
    881530 83 57 34 20 1.4
    881577 89 71 39 20 1.9
    881578 67 48 32 18 0.8
    881597 83 69 49 30 2.4
    881717 70 46 20 15 0.8
    881718 91 62 31 20 1.6
    881741 73 49 24 16 0.9
    881742 64 42 22 14 0.6
    881973 79 58 43 35 2.0
    882352 112 59 36 16 1.9
    882725 90 68 43 20 2.0
    882749 94 83 49 23 2.7
    882797 69 52 27 16 0.9
    882819 97 82 61 28 3.5
    882866 136 119 65 28 4.5
  • TABLE 74
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC) IC50
    Number 296 nM 888 nM 2,666 nM 8,000 nM (μM)
    609408 96 45 25 15 1.3
    881127 100 72 44 21 2.3
    881317 74 48 33 18 1.0
    881389 79 67 42 23 1.8
    881413 59 43 35 20 0.6
    881414 97 79 37 20 2.2
    881437 91 67 36 21 1.8
    881581 62 43 27 21 0.6
    881671 80 66 47 41 3.1
    881743 68 55 30 24 1.0
    881791 81 61 34 13 1.3
    882069 74 60 39 30 1.6
    882070 81 60 42 33 2.0
    882162 79 67 42 17 1.6
    882185 73 50 24 22 1.0
    882282 65 38 22 14 0.6
    882305 62 43 15 19 0.5
    882376 97 88 61 33 4.1
    882377 82 46 22 13 1.0
  • TABLE 75
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC) IC50
    Number 296 nM 888 nM 2,666 nM 8,000 nM (μM)
    609408 69 41 21 11 0.7
    881391 100 67 36 21 2.0
    881439 76 48 32 19 1.1
    881511 82 73 36 26 2.0
    881558 70 49 29 14 0.9
    881582 61 42 21 15 0.5
    881601 92 76 47 18 2.2
    881648 78 68 36 21 1.6
    881672 66 51 30 18 0.8
    881744 95 78 43 19 2.2
    881746 69 41 26 15 0.7
    881975 101 91 63 51 >8.0
    881999 71 53 31 26 1.1
    882210 91 78 50 22 2.5
    882283 79 55 29 17 1.2
    882354 81 57 34 20 1.4
    882379 108 86 60 25 3.4
    882800 77 55 28 15 1.1
    882870 69 42 23 12 0.7
  • TABLE 76
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC) IC50
    Number 296 nM 888 nM 2,666 nM 8,000 nM (μM)
    609408 81 47 29 18 1.1
    881296 84 60 57 38 3.2
    881440 75 74 46 26 2.2
    881441 93 68 34 26 2.0
    881465 85 63 38 29 1.9
    881512 82 60 38 27 1.7
    881559 84 62 47 31 2.2
    881747 80 57 37 26 1.5
    881955 73 66 35 30 1.6
    882072 82 73 51 32 2.8
    882142 85 68 48 31 2.5
    882214 77 46 30 13 1.0
    882309 74 54 51 24 1.6
    882310 81 35 31 14 0.9
    882357 74 58 35 31 1.5
    882495 93 76 52 33 3.2
    882565 90 77 55 33 3.3
    882777 96 75 35 33 2.5
    882871 67 49 44 21 1.1
  • TABLE 77
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC) IC50
    Number 296 nM 888 nM 2,666 nM 8,000 nM (μM)
    609408 83 48 25 15 1.1
    881322 98 71 42 17 2.0
    881371 91 70 37 22 1.9
    881394 77 47 27 14 1.0
    881395 77 49 26 15 1.0
    881442 51 36 22 9 0.3
    881514 88 75 46 21 2.2
    881561 92 62 38 18 1.7
    881585 76 52 34 23 1.2
    881724 100 72 39 22 2.2
    881748 81 61 34 20 1.5
    881749 70 46 27 12 0.8
    881773 88 59 33 20 1.5
    882215 83 60 50 26 2.0
    882311 82 63 36 21 1.6
    882358 80 52 32 17 1.2
    882359 91 57 34 11 1.4
    882383 92 86 64 37 4.8
    882429 74 52 32 11 1.0
  • TABLE 78
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC) IC50
    Number 296 nM 888 nM 2,666 nM 8,000 nM (μM)
    609408 85 53 36 14 1.3
    881133 101 88 76 63 >8.0
    881204 92 79 50 26 2.7
    881396 71 46 29 16 0.9
    881515 90 67 44 21 2.0
    881516 81 49 35 17 1.2
    881588 69 52 26 18 0.9
    881726 73 42 44 8 1.0
    881727 66 50 35 19 0.9
    881750 73 49 19 17 0.9
    882077 93 78 54 37 3.7
    882099 61 46 18 23 0.6
    882169 101 84 51 18 2.6
    882170 92 76 39 25 2.2
    882313 87 60 32 18 1.5
    882384 93 68 40 18 1.9
    882408 84 61 41 19 1.6
    882709 104 106 108 98 >8.0
    882758 82 53 36 17 1.3
  • TABLE 79
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC) IC50
    Number 296 nM 888 nM 2,666 nM 8,000 nM (μM)
    609408 83 49 25 10 1.1
    881279 87 73 43 22 2.1
    881399 79 49 23 24 1.1
    881422 85 63 44 29 2.1
    881470 109 92 54 19 3.0
    881494 68 50 33 20 0.9
    881495 68 46 24 17 0.8
    881517 75 41 14 12 0.7
    881542 76 55 31 13 1.1
    881589 80 48 26 10 1.0
    881607 90 64 32 19 1.6
    881608 73 45 22 21 0.8
    881728 58 32 17 11 0.4
    881729 94 75 40 29 2.4
    881752 75 47 28 14 0.9
    882409 86 66 42 20 1.8
    882432 101 67 34 12 1.7
    882433 72 38 25 16 0.7
    882806 92 35 45 34 1.7
  • TABLE 80
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC) IC50
    Number 296 nM 888 nM 2,666 nM 8,000 nM (μM)
    609408 99 55 43 12 1.7
    690521 88 58 36 21 1.6
    881112 133 107 73 56 >8.0
    881183 109 93 58 31 3.9
    881280 94 61 40 23 1.9
    881303 90 79 55 28 3.0
    881304 94 86 86 37 7.9
    881327 125 115 71 44 6.9
    881448 82 58 36 21 1.5
    881496 72 55 34 21 1.2
    881543 86 67 37 24 1.8
    881610 71 49 22 13 0.8
    881657 83 61 46 29 2.0
    881658 77 53 29 13 1.1
    881753 81 70 48 20 2.0
    881962 87 67 49 29 2.5
    882268 110 72 50 31 3.0
    882479 96 81 45 42 3.7
    882761 76 67 37 25 1.6
  • TABLE 81
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC) IC50
    Number 296 nM 888 nM 2,666 nM 8,000 nM (μM)
    609408 87 48 28 15 1.2
    690522 63 32 13 11 0.4
    690523 90 61 37 19 1.7
    881281 95 69 49 32 2.8
    881305 76 60 42 23 1.6
    881425 71 53 34 21 1.1
    881426 73 45 29 19 0.9
    881449 65 50 28 16 0.8
    881497 129 95 57 19 3.3
    881498 98 71 34 16 1.9
    881659 53 25 13 9 <0.3
    881660 65 32 17 10 0.5
    881683 74 60 37 22 1.4
    881780 82 54 34 17 1.3
    881963 91 66 39 33 2.3
    882175 79 43 24 12 0.9
    882246 69 44 29 11 0.8
    882810 100 66 45 25 2.3
    882833 101 86 57 23 3.1
  • TABLE 82
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC) IC50
    Number 296 nM 888 nM 2,666 nM 8,000 nM (μM)
    609408 87 51 28 14 1.2
    881258 115 91 60 31 3.9
    881282 104 89 42 32 3.1
    881404 89 81 43 27 2.5
    881427 87 65 48 19 1.9
    881450 63 42 26 12 0.6
    881451 100 77 49 30 2.9
    881452 77 67 49 27 2.2
    881499 84 74 44 35 2.7
    881661 122 92 51 23 3.2
    881684 106 89 55 33 3.8
    881733 82 63 32 29 1.7
    881734 72 49 34 23 1.0
    881941 94 86 60 41 5.2
    882177 94 62 35 30 2.0
    882199 90 81 38 16 2.0
    882200 89 60 36 22 1.7
    882247 79 60 47 33 2.2
    882765 101 82 57 30 3.5
  • TABLE 83
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC) IC50
    Number 296 nM 888 nM 2,666 nM 8,000 nM (μM)
    609408 87 49 30 11 1.2
    881213 85 67 50 20 2.1
    881238 83 58 33 19 1.4
    881286 64 51 35 22 0.9
    881381 77 55 34 26 1.3
    881382 83 71 49 37 3.0
    881405 86 58 42 16 1.6
    881477 80 62 56 28 2.4
    881478 102 69 47 30 2.7
    881571 109 90 47 27 3.1
    881572 87 67 39 25 1.9
    881616 104 76 47 36 3.3
    881663 130 108 63 32 4.6
    881784 117 87 50 35 3.7
    882085 82 66 46 27 2.1
    882107 109 83 74 37 5.5
    882178 114 69 36 16 2.1
    882601 123 99 64 26 4.0
    882670 91 85 66 34 4.7
  • TABLE 84
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC) IC50
    Number 296 nM 888 nM 2,666 nM 8,000 nM (μM)
    609408 101 60 32 14 1.6
    881240 103 79 47 23 2.6
    881359 124 89 57 35 4.1
    881360 83 58 40 22 1.6
    881384 85 72 42 39 2.8
    881432 73 62 49 29 2.0
    881575 92 67 52 40 3.4
    881593 84 71 57 31 3.1
    881761 94 93 72 56 >8.0
    882039 95 79 68 50 >8.0
    882086 96 79 50 25 2.7
    882087 72 55 36 32 1.4
    882204 67 77 38 30 1.9
    882227 111 90 54 47 5.2
    882228 96 75 52 40 3.8
    882323 106 87 62 34 4.3
    882532 114 85 54 33 3.7
    882721 98 78 69 45 6.6
    882744 84 79 50 31 2.9
  • Example 15: Effect of Modified Oligonucleotides on Human IRF4 In Vitro, Multiple Doses
  • Modified oligonucleotides selected from the examples above were tested at various doses in MM.1R cells. Cells were plated at a density of 5,000 cells per well and transfected by free uptake with 74 nM, 222 nM, 666 nM, and 2,000 nM concentrations of modified oligonucleotide, as specified in the tables below. After a treatment period of approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR. Human IRF4 primer probe set hIRF4_LTS34726 (described hereinabove in Example 7) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen. Results are presented as the percent level of IRF4 mRNA transcript, relative to that of untreated control (UTC) cells. As illustrated in the tables below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • TABLE 85
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC) IC50
    Number 74 nM 222 nM 666 nM 2,000 nM (μM)
    609408 86 66 43 17 0.4
    935580 89 62 34 10 0.4
    935603 91 69 46 23 0.5
    935620 84 64 37 15 0.4
    935658 82 56 37 15 0.3
    935898 74 47 24 7 0.2
    935911 100 88 66 43 1.5
    935918 90 75 45 23 0.6
    935921 80 52 27 9 0.3
    935925 98 67 62 36 0.9
    935928 90 72 48 23 0.6
    935929 96 85 60 36 1.1
    935935 95 83 63 32 1.0
    935939 86 74 50 41 0.9
    935941 86 84 70 41 1.7
    935948 86 62 45 24 0.5
    935958 83 56 33 14 0.3
    935961 78 51 27 8 0.3
    935968 88 61 35 12 0.4
  • TABLE 86
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC) IC50
    Number 74 nM 222 nM 666 nM 2,000 nM (μM)
    609408 79 59 37 14 0.3
    935581 78 61 38 15 0.4
    935608 85 71 48 20 0.5
    935655 93 88 70 46 >2.0
    935679 92 72 47 23 0.6
    935689 86 63 40 19 0.4
    935696 72 45 22 9 0.2
    935697 80 55 23 9 0.3
    935698 83 68 39 17 0.4
    935699 87 60 36 14 0.4
    935700 72 59 26 7 0.3
    935701 82 64 40 18 0.4
    935707 84 68 49 23 0.5
    935708 84 59 34 15 0.4
    935721 86 70 46 24 0.5
    935724 73 39 20 5 0.2
    935727 85 67 49 27 0.6
    935734 74 58 35 16 0.3
    935741 85 68 42 17 0.4
  • TABLE 87
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC) IC50
    Number 74 nM 222 nM 666 nM 2,000 nM (μM)
    609408 77 60 41 16 0.4
    935668 94 78 51 25 0.7
    935671 91 73 54 27 0.7
    935686 90 69 53 34 0.8
    935709 72 78 57 36 0.9
    935731 80 66 52 36 0.7
    935762 72 56 35 19 0.3
    935765 75 55 37 15 0.3
    935772 81 65 51 27 0.6
    935779 78 72 55 28 0.7
    935782 66 55 36 15 0.2
    935789 81 77 58 32 0.9
    935795 95 77 60 33 0.9
    935805 85 68 42 21 0.5
    935850 74 48 25 12 0.2
    935851 78 54 26 9 0.3
    935854 79 64 35 14 0.3
    935857 78 66 44 19 0.4
    935878 71 42 24 10 0.2
  • TABLE 88
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC) IC50
    Number 74 nM 222 nM 666 nM 2,000 nM (μM)
    609408 79 62 39 15 0.4
    881450 100 75 56 28 0.8
    881659 76 45 21 5 0.2
    935824 86 65 46 23 0.5
    935833 81 60 44 26 0.5
    935840 82 54 51 27 0.5
    935853 85 64 45 21 0.5
    935856 92 71 50 29 0.7
    935859 90 81 63 36 1.1
    935888 79 72 43 20 0.5
    936006 80 64 41 21 0.4
    936007 87 65 34 13 0.4
    936011 94 79 62 40 1.2
    936013 78 67 48 26 0.5
    936016 83 62 43 21 0.4
    936018 82 66 43 17 0.4
    936033 80 63 47 25 0.5
    936039 85 67 48 25 0.5
    936046 88 66 49 30 0.6
  • Example 16: Effect of Modified Oligonucleotides on Human IRF4 In Vitro, Multiple Doses
  • Modified oligonucleotides selected from the examples above were tested at various doses in MM.1R cells. Cells were plated at a density of 5,000 cells per well and transfected by free uptake with 74 nM, 222 nM, 666 nM, and 2,000 nM concentrations of modified oligonucleotide, as specified in the tables below. After a treatment period of approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR. Human IRF4 primer probe set hIRF4_LTS34726 (described hereinabove in Example 7) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen. Results are presented as the percent level of IRF4 mRNA transcript, relative to that of untreated control (UTC) cells. As illustrated in the tables below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • TABLE 89
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 74 nM 222 nM 666 nM 2,000 nM
    609311 94 106 100 87
    609312 97 96 103 93
    609328 87 86 88 83
    609337 94 98 99 96
    609354 93 88 76 50
    609357 101 87 90 61
    609408 83 57 35 11
    609422 96 100 90 76
    609530 103 94 94 87
    609533 103 103 91 75
    609546 100 103 107 97
    609591 93 94 89 68
    609592 95 94 88 76
  • TABLE 90
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 74 nM 222 nM 666 nM 2,000 nM
    609408 93 61 37 12
    609592 97 85 88 81
    609594 98 97 81 85
    881127 96 98 87 66
    881183 93 89 75 55
    881193 25 21 17 13
    881204 97 82 49 26
    881955 97 73 44 16
    881962 119 96 93 67
    881963 104 119 104 91
    881973 99 95 89 74
    881999 98 91 80 46
    882066 108 103 104 94
    882069 109 99 91 65
    882070 108 106 81 68
    882072 112 104 94 72
    882077 107 122 101 102
    882085 96 85 71 37
    882086 90 77 50 17
  • TABLE 91
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 74 nM 222 nM 666 nM 2,000 nM
    609408 84 68 36 12
    882087 84 75 52 23
    882142 95 99 82 68
    882162 87 94 76 49
    882169 97 79 59 41
    882170 86 77 60 28
    882175 98 101 72 46
    882177 94 96 80 60
    882178 103 105 109 95
    882185 100 95 87 63
    882199 98 105 98 85
    882200 111 118 101 87
    882204 101 96 78 61
    882214 113 106 96 80
    882215 112 113 110 104
    882227 114 100 109 90
    882228 101 92 85 63
    882247 114 105 104 102
    882268 108 94 89 67
  • TABLE 92
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 74 nM 222 nM 666 nM 2,000 nM
    609408 81 69 39 9
    882283 98 94 86 54
    882309 85 93 79 49
    882310 91 94 85 92
    882311 83 74 59 18
    882313 87 73 57 25
    882323 92 95 81 50
    882325 99 87 62 31
    882326 100 98 100 68
    882352 93 91 78 62
    882354 96 93 78 66
    882357 103 84 78 48
    882358 90 74 42 13
    882359 109 112 104 91
    882376 104 107 97 86
    882377 98 94 89 64
    882379 101 101 108 101
    882383 106 112 104 104
    882384 101 98 80 62
  • TABLE 93
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 74 nM 222 nM 666 nM 2,000 nM
    609408 74 64 38 13
    882398 81 74 63 28
    882408 88 77 64 37
    882409 101 67 89 92
    882429 98 90 90 89
    882432 88 93 91 83
    882479 86 91 89 56
    882495 83 100 96 87
    882532 89 101 126 N/A
    882565 107 109 109 92
    882601 103 98 85 91
    882670 104 95 91 60
    882721 98 97 91 73
    882725 93 92 80 72
    882744 100 66 73 48
    882749 89 92 77 55
    882758 88 79 72 56
    882761 87 88 77 61
    882765 89 103 94 98
  • TABLE 94
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 74 nM 222 nM 666 nM 2,000 nM
    609408 54 34 41 N/A
    881450 65 59 29 11
    881659 45 19 6 2
    882777 109 133 93 105
    882797 113 106 93 63
    882800 112 83 56 22
    882806 100 115 107 91
    882810 88 88 84 50
  • Example 17: Design of 3-10-3 cEt Gapmers with Phosphorothioate Internucleoside Linkages
  • Modified oligonucleotides complementary to a human IRF4 nucleic acid were designed. The modified oligonucleotides in Table 95 are 3-10-3 cEt gapmers. The gapmers are 16 nucleobases in length, wherein the central gap segment comprises ten 2′-deoxynucleosides and is flanked by wing segments on both the 5′ end and on the 3′ end comprising three cEt nucleosides. The sugar motif for the gapmers is (from 5′ to 3′): kkkddddddddddkkk; wherein represents a 2′-deoxyribose sugar and ‘k’ represents a cEt modified sugar. Each internucleoside linkage is a phosphorothioate internucleoside linkage and each cytosine residue is a 5-methylcytosine. “Start Site” indicates the 5′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence. “Stop Site” indicates the 3′-most nucleoside to which the gapmer is complementary in the human nucleic acid sequence.
  • Each modified oligonucleotide listed in Table 95 below is complementary to human IRF4 nucleic acid sequences SEQ ID NO: 1 or SEQ ID NO: 2, as indicated. ‘N/A’ indicates that the modified oligonucleotide is not complementary to that particular nucleic acid sequence with 100% complementarity.
  • TABLE 95
    Dose-dependent reduction of human IRF4 mRNA by modified oligonucleotides
    Compound SEQ ID NO: 1 SEQ ID NO: 1 SEQ ID NO: 2 SEQ ID NO: 2 SEQ
    Number Start Site Stop Site Start Site Stop Site Sequence ID NO
    970454 N/A N/A 17700 17715 AGAACATTACGAGAGG 3371
    970466 N/A N/A 18074 18089 GGTTGGCTGGTCTTTG 3337
    970500 N/A N/A 18088 18103 ATTATATACTGGTTGG 3340
    970524 N/A N/A 18248 18263 CGATCATCAACTTCTT 3372
    970527 N/A N/A 18572 18587 GTGATAGCTGAGCTGA 3343
    970539 N/A N/A 18583 18598 ACTGGATTGATGTGAT 3373
    970545 N/A N/A 18718 18733 GGAACTCATAGGTGTA 3374
    970546 1415 1430 19532 19547 CTGATGTGTTCTGGTA 3375
    970547 N/A N/A 17235 17250 TACGCTTATTTTTCCA 3376
    970548 N/A N/A 17474 17489 GCAATCTTAACCTGGA 3377
    970552 N/A N/A 18580 18595 GGATTGATGTGATAGC 3378
    970554 N/A N/A 19020 19035 TCTGTATAGTTCTCAA 3379
    970574 1350 1365 19467 19482 TAGTTGTCTGGCTAGC 3380
    970597 N/A N/A 18575 18590 GATGTGATAGCTGAGC 3346
    970598 N/A N/A 18612 18627 CAGTGACTTGCATCCA 3350
    970600 1346 1361 19463 19478 TGTCTGGCTAGCAGAG 3381
    970602 1396 1411 19513 19528 CGTAGCCCCTCAGGAA 3382
    970603 1423 1438 19540 19555 CTGGATTGCTGATGTG 3383
  • Example 18: Effect of Modified Oligonucleotides on Human IRF4 In Vitro, Multiple Doses
  • Modified oligonucleotides selected from the examples above were tested at various doses in MM.1R cells. Cells were plated at a density of 5,000 cells per well and transfected by free uptake with 62.5 nM, 250 nM, 1,000 nM, and 4,000 nM concentrations of modified oligonucleotide, as specified in the tables below. After a treatment period of approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR. Human IRF4 primer probe set hIRF4_LTS34726 (described hereinabove in Example 7) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen. Results are presented as the percent level of IRF4 mRNA transcript, relative to that of untreated control (UTC) cells. As illustrated in the tables below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • TABLE 96
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 62.5 nM 250 nM 1,000 nM 4,000 nM
    609408 84 55 28 7
    935583 99 77 32 8
    969936 86 88 61 34
    969937 94 100 75 33
    969938 104 84 60 30
    970044 115 107 79 42
    970069 86 111 97 67
    970104 101 87 60 30
    970114 109 96 73 45
    970117 109 84 48 19
    970139 78 60 44 24
    970158 101 102 81 46
    970159 82 64 45 18
    970189 85 66 42 25
    970217 96 90 71 44
    970228 65 77 37 13
    970253 111 105 100 63
    970344 83 117 124 92
    970388 100 87 70 29
  • TABLE 97
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 62.5 nM 250 nM 1,000 nM 4,000 nM
    609408 92 55 28 8
    969879 106 110 107 113
    969933 94 71 48 36
    969991 115 92 56 13
    970013 96 78 48 19
    970043 102 82 43 16
    970103 96 64 52 34
    970160 111 96 75 35
    970161 106 104 82 62
    970162 94 82 60 18
    970211 93 79 59 32
    970212 97 80 38 7
    970230 110 105 84 52
    970231 113 105 114 94
    970249 116 93 59 22
    970358 113 110 87 55
    970370 107 93 77 32
    970382 113 97 70 40
    970610 125 103 88 50
  • TABLE 98
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 62.5 nM 250 nM 1,000 nM 4,000 nM
    609408 84 56 30 7
    970454 98 84 59 35
    970466 102 84 51 34
    970500 97 85 61 23
    970524 76 50 28 8
    970527 87 62 30 11
    970539 98 94 75 35
    970545 89 74 47 25
    970546 86 73 55 31
    970547 99 71 49 35
    970548 103 92 63 30
    970552 93 76 41 12
    970554 102 84 58 31
    970574 96 84 68 32
    970597 38 21 15 8
    970598 60 57 47 25
    970600 49 35 29 21
    970602 41 39 32 19
    970603 55 47 44 17
  • Example 19: Effect of Modified Oligonucleotides on Human IRF4 In Vitro, Multiple Doses
  • Modified oligonucleotides selected from the examples above were tested at various doses in MM.1R cells. Cells were plated at a density of 5,000 cells per well and transfected by free uptake with 62.5 nM, 250 nM, 1,000 nM, and 4,000 nM concentrations of modified oligonucleotide, as specified in the tables below. After a treatment period of approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR. Human IRF4 primwr probe set RTS4523 (forward sequence AAGCCTTGGCGTTCTCAGACT, designated herein as SEQ ID NO: 3386; reverse sequence TCAGCTCCTTCACGAGGATTTC, designated herein as SEQ ID NO: 3387; probe sequence CCGGCTGCACATCTGCCTGTACTACC, designated herein as SEQ ID: 3388), was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen. Results are presented as the percent level of IRF4 mRNA transcript, relative to that of untreated control (UTC) cells. As illustrated in the table below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • TABLE 99
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 62.5 nM 250 nM 1,000 nM 4,000 nM
    609408 75 51 31 10
    970454 88 80 49 34
    970466 85 80 65 30
    970500 91 75 43 26
    970524 77 50 25 7
    970527 83 53 25 12
    970539 91 80 61 31
    970545 68 58 35 20
    970546 64 59 47 30
    970547 88 56 44 23
    970548 97 92 62 29
    970552 76 80 40 12
    970554 100 74 60 29
    970574 93 76 67 32
    970597 93 99 78 51
    970598 80 76 62 39
    970600 82 87 80 63
    970602 85 80 66 41
    970603 83 77 64 29
  • Example 20: Effect of Modified Oligonucleotides on Human IRF4 In Vitro, Multiple Doses
  • Modified oligonucleotides selected from the examples above were tested at various doses in MM.1R cells. Cells were plated at a density of 5,000 cells per well and transfected by free uptake with 62.5 nM, 250 nM, 1,000 nM, and 4,000 nM concentrations of modified oligonucleotide, as specified in the tables below. After a treatment period of approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR. Human IRF4 primer probe set hIRF4_LTS34726 (described hereinabove in Example 7) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen. Results are presented as the percent level of IRF4 mRNA transcript, relative to that of untreated control (UTC) cells. As illustrated in the tables below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • TABLE 100
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 62.5 nM 250 nM 1,000 nM 4,000 nM
    609408 72 43 19 4
    881955 89 69 40 10
    881962 107 92 66 23
    881963 116 116 99 88
    881973 109 101 86 59
    881999 117 98 72 32
    882066 110 114 107 105
    882069 100 95 75 43
    882070 101 94 82 42
    882072 95 98 83 59
    882077 101 96 90 68
    882085 96 71 49 13
    882086 92 68 37 8
    882087 98 74 45 13
    882142 103 89 80 56
    882162 94 80 61 27
    882169 102 93 93 77
    882170 99 84 71 35
    882175 89 75 45 21
  • TABLE 101
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 62.5 nM 250 nM 1,000 nM 4,000 nM
    609408 73 43 19 4
    882177 83 66 38 11
    882178 101 100 87 59
    882185 99 90 73 41
    882199 108 111 96 82
    882200 112 106 97 66
    882204 96 82 55 22
    882214 98 92 53 12
    882215 118 112 117 106
    882228 89 75 46 15
    882246 101 98 85 58
    882247 97 101 92 74
    882268 101 88 78 49
    882283 104 95 86 48
    882309 87 76 59 31
    882310 96 103 105 107
    882311 99 99 119 99
    882313 98 82 61 31
    882323 89 89 81 68
  • TABLE 102
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 62.5 nM 250 nM 1,000 nM 4,000 nM
    609408 74 49 23 5
    882325 94 95 85 45
    882326 101 98 86 64
    882352 97 88 75 48
    882354 103 91 52 38
    882357 106 91 68 36
    882358 96 92 74 37
    882359 98 99 94 64
    882377 104 99 82 43
    882384 96 82 67 39
    882398 85 63 36 10
    882408 91 68 41 11
    882409 105 94 75 44
    882429 105 99 90 74
    882432 101 102 102 103
    882479 98 99 94 83
    882495 97 94 89 74
    882532 93 92 78 41
    882565 100 99 94 88
  • TABLE 103
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 62.5 nM 250 nM 1,000 nM 4,000 nM
    609408 77 50 23 6
    881955 92 75 43 11
    881962 96 91 64 26
    881963 95 100 93 76
    882725 102 102 96 78
    882744 104 107 93 74
    882749 102 94 79 55
    882758 108 94 76 44
    882761 106 99 77 47
    882765 99 89 61 34
    882777 105 111 108 90
    882797 107 96 78 44
    882800 89 68 36 9
    882806 99 96 84 60
    882810 94 93 65 31
    882833 101 102 83 67
    882870 98 88 69 34
    882871 103 90 75 55
    882898 101 88 72 45
  • Example 21: Effect of Modified Oligonucleotides on Human IRF4 In Vitro, Multiple Doses
  • Modified oligonucleotides selected from the examples above were tested at various doses in MM.1R cells. Cells were plated at a density of 5,000 cells per well and transfected by free uptake with 62.5 nM, 250 nM, 1,000 nM, and 4,000 nM concentrations of modified oligonucleotide, as specified in the tables below. After a treatment period of approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR. Human IRF4 primer probe set RTS4523 (described hereinabove in Example 19) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen. Results are presented as the percent level of IRF4 mRNA transcript, relative to that of untreated control (UTC) cells. As illustrated in the table below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • TABLE 104
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 62.5 nM 250 nM 1,000 nM 4,000 nM
    609408 84 47 22 5
    881955 82 64 33 8
    881962 109 79 63 25
    881963 99 78 74 66
    882725 85 72 76 60
    882744 85 104 80 60
    882749 114 95 64 50
    882758 111 98 67 37
    882761 114 108 75 32
    882765 85 75 52 27
    882777 83 95 79 63
    882797 80 72 59 40
    882800 53 60 28 7
    882806 108 95 78 55
    882810 128 119 69 34
    882833 94 91 75 69
    882870 114 97 71 31
    882871 79 82 55 40
    882898 81 73 58 34
  • Example 22: Effect of Modified Oligonucleotides on Human IRF4 In Vitro, Multiple Doses
  • Modified oligonucleotides selected from the examples above were tested at various doses in MM.1R cells. Cells were plated at a density of 5,000 cells per well and transfected by free uptake with 62.5 nM, 250 nM, 1,000 nM, and 4,000 nM concentrations of modified oligonucleotide, as specified in the tables below. After a treatment period of approximately 24 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR. Human IRF4 primer probe set RTS4522 (described hereinabove in Example 11) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen. Results are presented as the percent level of IRF4 mRNA transcript, relative to that of untreated control (UTC) cells. As illustrated in the tables below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • TABLE 105
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC) IC50
    Number 62.5 nM 250 nM 1,000 nM 4,000 nM (μM)
    609408 61 41 26 12 0.1
    881450 68 59 41 26 0.4
    881659 59 34 16 9 0.1
    1013053 63 50 32 16 0.2
    1013074 89 71 49 14 0.7
    1013492 66 46 36 21 0.2
    1013513 72 64 37 21 0.4
    1013514 81 68 41 15 0.5
    1013647 66 56 37 18 0.3
    1013933 92 78 44 13 0.7
    1013953 97 62 40 13 0.6
    1014087 82 67 40 28 0.7
    1014088 59 44 32 15 0.2
    1014095 42 35 24 12 <0.1
    1014097 79 57 40 17 0.4
    1014393 60 49 26 9 0.2
    1014394 46 38 28 9 <0.1
    1014412 85 57 44 23 0.6
    1014834 50 40 22 9 <0.1
  • TABLE 106
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC) IC50
    Number 62.5 nM 250 nM 1,000 nM 4,000 nM (μM)
    609408 63 46 28 15 0.2
    881659 58 32 16 9 0.1
    935607 57 41 28 16 0.1
    1012795 66 43 26 7 0.2
    1012819 92 75 35 25 0.7
    1012821 52 38 28 11 0.1
    1012836 103 69 44 19 0.8
    1012882 94 60 31 11 0.5
    1012883 60 42 28 11 0.1
    1012884 49 39 25 14 <0.1
    1012900 90 72 42 22 0.7
    1012914 55 42 25 10 0.1
    1014968 56 48 35 16 0.2
    1014976 76 43 37 14 0.3
    1015254 68 46 31 14 0.2
    1015275 86 61 24 12 0.4
    1015409 66 53 34 16 0.3
    1015417 76 56 37 16 0.4
    1015716 59 46 24 10 0.1
  • Example 23: Effect of Modified Oligonucleotides on Human IRF4 In Vitro, Multiple Doses
  • Modified oligonucleotides selected from the examples above were tested at various doses in KMS11 cells for their effects on target knockdown and on cell line proliferation.
  • Target Knockdown
  • KMS11 cells were plated at a density of 10,000 cells per well and transfected by free uptake with 8 nM, 40 nM, 200 nM, and 1,000 nM concentrations of modified oligonucleotide, as specified in the tables below. After a treatment period of approximately 48 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR. Human IRF4 primer probe set RTS4522 (described hereinabove in Example 11) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen. Results are presented as the percent level of IRF4 mRNA transcript, relative to that of untreated control (UTC) cells. As illustrated in the tables below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • TABLE 107
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 8 nM 40 nM 200 nM 1,000 nM
    609408 79 67 38 14
    935762 79 41 17 10
    935918 71 35 14 10
    936007 81 67 25 14
    970527 90 53 23 15
    882085 86 56 24 11
    882408 74 70 37 17
  • TABLE 108
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 8 nM 40 nM 200 nM 1,000 nM
    609408 92 69 30 13
    882800 78 52 24 10
    969933 96 88 72 61
    1012795 70 41 18 9
    1012821 84 53 39 20
    1012884 85 51 26 17
    1014095 82 41 19 10
  • TABLE 109
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 8 nM 40 nM 200 nM 1,000 nM
    609408 89 67 30 14
    1014393 80 50 22 12
    1014394 86 74 38 19
    1014834 86 51 17 9
    1015716 95 78 43 17
    881413 92 64 35 13
    881449 94 85 48 22
  • TABLE 110
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 8 nM 40 nM 200 nM 1,000 nM
    609408 98 78 33 15
    935658 87 61 23 13
    935696 90 48 17 11
    935898 103 81 50 31
    935928 92 48 17 11
    935968 95 52 17 11
    936006 99 81 38 19
  • Proliferation
  • KMS11 cells were plated at a density of 2,000 cells per well and transfected by free uptake with 8 nM, 40 nM, 200 nM, and 1,000 nM concentrations of modified oligonucleotide, as specified in the tables below. After seven days, CellTiterGlo-2.0 (Promega) was added and luminescence was measured on Glomax (Promega).
  • TABLE 111
    Dose-dependent reduction of KMS11 proliferation
    by modified oligonucleotides
    Compound IRF4 proliferation (% UTC)
    Number 8 nM 40 nM 200 nM 1,000 nM
    690890 93 79 22 7
    935762 89 34 9 6
    935918 85 28 8 7
    936007 93 66 20 8
    970527 92 50 11 5
    882085 97 55 11 6
    882408 95 68 25 10
  • TABLE 112
    Dose-dependent reduction of KMS11 proliferation
    by modified oligonucleotides
    Compound IRF4 proliferation (% UTC)
    Number 8 nM 40 nM 200 nM 1,000 nM
    690890 98 82 26 9
    882800 87 48 16 9
    969933 93 86 79 78
    1012795 89 25 4 1
    1012821 98 47 22 5
    1012884 104 61 24 12
    1014095 95 35 15 13
  • TABLE 113
    Dose-dependent reduction of KMS11 proliferation
    by modified oligonucleotides
    Compound IRF4 proliferation (% UTC)
    Number 8 nM 40 nM 200 nM 1,000 nM
    690890 91 67 21 7
    1014393 89 45 15 9
    1014394 91 70 26 11
    1014834 86 43 12 6
    1015716 92 78 32 12
    881413 98 67 15 11
    881449 97 81 39 21
  • TABLE 114
    Dose-dependent reduction of KMS11 proliferation
    by modified oligonucleotides
    Compound IRF4 proliferation (% UTC)
    Number 8 nM 40 nM 200 nM 1,000 nM
    690890 90 77 22 8
    935658 91 51 11 7
    935696 86 29 7 6
    935898 96 82 56 38
    935928 94 45 9 7
    935968 94 49 10 5
    936006 97 80 26 12
  • Example 24: Effect of Modified Oligonucleotides on Human IRF4 In Vitro, Multiple Doses
  • Modified oligonucleotides selected from the examples above were tested at various doses in H929 cells for their effects on target knockdown and on cell line proliferation.
  • Target Knockdown
  • H929 cells were plated at a density of 10,000 cells per well and transfected by free uptake with 8 nM, 40 nM, 200 nM, and 1,000 nM concentrations of modified oligonucleotide or 0.67 nM, 2 nM, 6.67 nM or 20 nM concentrations of modified oligonucleotide, as specified in the tables below. After a treatment period of approximately 48 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR. Human IRF4 primer probe set RTS4522 (described hereinabove in Example 11) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen. Results are presented as the percent level of IRF4 mRNA transcript, relative to that of untreated control (UTC) cells. As illustrated in the tables below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • TABLE 115
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 8 nM 40 nM 200 nM 1,000 nM
    609408 88 66 39 34
    935762 76 47 29 31
    935918 70 43 34 24
    936007 85 62 39 32
    970527 83 49 41 24
    882085 107 70 48 16
    882408 99 88 59 42
  • TABLE 116
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 8 nM 40 nM 200 nM 1,000 nM
    609408 69 53 35 30
    882800 63 62 38 28
    969933 112 95 87 83
    1012795 72 67 45 31
    1012821 69 86 47 35
    1012884 82 88 51 32
    1014095 71 68 31 21
  • TABLE 117
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 8 nM 40 nM 200 nM 1,000 nM
    609408 88 57 31 37
    1014393 70 43 38 24
    1014394 83 60 43 32
    1014834 84 45 33 23
    1015716 88 75 46 17
    881413 86 67 46 24
    881449 109 90 63 51
  • TABLE 118
    Dose-dependent reduction of human IRF4
    mRNA by modified oligonucleotides
    Compound IRF4 expression (% UTC)
    Number 0.67 nM 2 nM 6.67 nM 20 nM
    609408 74 53 26 37
    935658 84 75 48 32
    935696 78 59 33 26
    935898 94 79 55 43
    935928 74 54 36 28
    935968 99 73 55 40
    936006 91 74 61 52
  • Proliferation
  • H929 cells were plated at a density of 2,000 cells per well and transfected by free uptake with 8 nM, 40 nM, 200 nM, and 1,000 nM concentrations of modified oligonucleotide, as specified in the tables below. After seven days, CellTiterGlo-2.0 (Promega) was added and luminescence was measured on Glomax (Promega).
  • TABLE 119
    Dose-dependent reduction of H929 proliferation
    by modified oligonucleotides
    Compound IRF4 proliferation (% UTC)
    Number 8 nM 40 nM 200 nM 1,000 nM
    690890 94 69 32 12
    935762 71 27 16 3
    935918 87 58 26 2
    936007 89 64 26 3
    970527 95 58 15 1
    882085 96 65 24 1
    882408 88 65 45 9
  • TABLE 120
    Dose-dependent reduction of H929 proliferation
    by modified oligonucleotides
    Compound IRF4 proliferation (% UTC)
    Number 8 nM 40 nM 200 nM 1,000 nM
    690890 73 75 21 6
    882800 89 87 30 4
    969933 92 90 77 77
    1012795 89 86 36 4
    1012821 95 86 41 13
    1012884 68 62 9 2
    1014095 78 63 22 5
  • TABLE 121
    Dose-dependent reduction of H929 proliferation
    by modified oligonucleotides
    Compound IRF4 proliferation (% UTC)
    Number 8 nM 40 nM 200 nM 1,000 nM
    690890 86 74 48 30
    1014393 95 65 30 2
    1014394 77 53 35 6
    1014834 89 61 34 2
    1015716 99 74 31 2
    881413 85 53 33 4
    881449 94 76 54 25
  • TABLE 122
    Dose-dependent reduction of H929 proliferation
    by modified oligonucleotides
    Compound IRF4 proliferation (% UTC)
    Number 8 nM 40 nM 200 nM 1,000 nM
    690890 92 79 52 30
    935658 95 62 23 7
    935696 84 60 32 3
    935898 101 87 62 26
    935928 75 50 25 6
    935968 96 66 40 10
    936006 98 73 38 9
  • Example 25: Effect of Modified Oligonucleotides on Human IRF4 In Vitro, Multiple Doses
  • Modified oligonucleotides selected from the examples above were tested at various doses in ABC-DLBCL lines U2932 and TMD8 for their effects on target knockdown and on cell line proliferation.
  • Target Knockdown
  • Cells were plated at a density of 10,000 cells per well and transfected by free uptake with 50 nM, 200 nM, 1,000 nM, or 5,000 nM concentrations of modified oligonucleotide, as specified in the tables below. Control oligonucleotide ION 792169, a 3-10-3 cEt gapmer with the sequence CGCCGATAAGGTACAC (SEQ ID NO: 3384), was also included. After a treatment period of approximately 48 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR. Human IRF4 primer probe set RTS4522 (described hereinabove in Example 11) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen. Results are presented as the percent level of IRF4 mRNA transcript, relative to untreated control (UTC) cells. As illustrated in the tables below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • TABLE 123
    Dose-dependent reduction of IRF4 expression
    by modified oligonucleotides in U2932 cells
    Compound IRF4 expression (% UTC)
    Number 50 nM 200 nM 1,000 nM 5,000 nM
    792169 98 102 102 99
    690890 84 64 55 38
    882800 85 63 51 38
    695696 71 62 54 49
    695968 84 70 55 43
    695918 83 64 47 33
  • TABLE 124
    Dose-dependent reduction of IRF4 expression
    by modified oligonucleotides in TMD8 cells
    Compound IRF4 expression (% UTC)
    Number 50 nM 200 nM 1,000 nM 5,000 nM
    792169 115 99 99 91
    690890 97 75 53 26
    882800 97 64 38 19
    695696 94 68 45 29
    695968 95 63 46 25
    695918 105 65 44 24
  • Proliferation
  • Cells were plated at a density of 2,000 cells per well and transfected by free uptake with 50 nM, 200 nM, 1,000 nM, or 5,000 nM concentrations of modified oligonucleotide, as specified in the tables below. After seven days, CellTiterGlo-2.0 (Promega) was added and luminescence was measured on Glomax (Promega).
  • TABLE 125
    Dose-dependent reduction of proliferation
    of U2932 cells by modified oligonucleotides
    Compound IRF4 proliferation (% UTC)
    Number 50 nM 200 nM 1,000 nM 5,000 nM
    792169 99 115 111 75
    690890 111 109 63 2
    882800 113 103 40 2
    695696 107 111 77 17
    695968 102 101 74 24
    695918 89 100 70 7
  • TABLE 126
    Dose-dependent reduction of proliferation
    of TMD8 cells by modified oligonucleotides
    Compound IRF4 proliferation (% UTC)
    Number 50 nM 200 nM 1,000 nM 5,000 nM
    792169 93 108 102 98
    690890 110 120 118 17
    882800 132 149 108 27
    695696 125 143 94 5
    695968 85 131 131 10
    695918 139 130 122 4
  • Example 26: Effect of Modified Oligonucleotides on Human IRF4 In Vitro, Multiple Doses
  • Modified oligonucleotides selected from the examples above were tested at various doses in ALCL cell lines for their effects on target knockdown and on cell line proliferation.
  • Target Knockdown
  • Cells were plated at a density of 10,000 cells per well and transfected by free uptake with 16 nM, 80 nM, or 400 nM concentrations of modified oligonucleotide, or 40 nM, 200 nM, 1,000 nM, or 5,000 nM concentrations of modified oligonucleotide, as specified in the tables below. After a treatment period of approximately 48 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR. Human IRF4 primer probe set RTS4522 (described hereinabove in Example 11) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen. Results are presented as the percent level of IRF4 mRNA transcript, relative to untreated control (UTC) cells. Control oligonucleotide 549148, a 3-10-3 cEt gapmer with the sequence GGCTACTACGCCGTCA (SEQ ID NO: 3385), was also included. As illustrated in the tables below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • TABLE 127
    Dose-dependent reduction of IRF4 expression by
    modified oligonucleotides in Karpas299 cells
    Compound IRF4 expression (% UTC)
    Number 16 nM 80 nM 400 nM 2,000 nM
    549148 92 85 86 83
    609408 85 65 39 23
    609416 82 75 66 53
  • TABLE 128
    Dose-dependent reduction of IRF4 expression
    by modified oligonucleotides in SupM2 cells
    Compound IRF4 expression (% UTC)
    Number 40 nM 200 nM 1,000 nM 5,000 nM
    549148 109 100 118 117
    609408 83 91 32 10
    609416 93 85 48 21
  • Proliferation
  • Cells were plated at a density of 2,000 cells per well and transfected by free uptake with 50 nM, 200 nM, 1,000 nM, or 5,000 nM concentrations of modified oligonucleotide, as specified in the tables below. After seven days, CellTiterGlo-2.0 (Promega) was added and luminescence was measured on Glomax (Promega).
  • TABLE 129
    Dose-dependent reduction of proliferation of
    Karpas299 cells by modified oligonucleotides
    Compound IRF4 proliferation (% UTC)
    Number 50 nM 200 nM 1,000 nM 5,000 nM
    549148 99 106 106 89
    609408 105 91 31 22
    609416 104 119 72 59
  • TABLE 130
    Dose-dependent reduction of proliferation
    of SupM2 cells by modified oligonucleotides
    Compound IRF4 proliferation (% UTC)
    Number 16 nM 80 nM 400 nM 2,000 nM
    549148 93 97 94 85
    609408 93 96 55 3
    609416 93 98 49 15
  • Example 27: Effect of Modified Oligonucleotides on Human IRF4 In Vitro, Multiple Doses
  • Modified oligonucleotides selected from the examples above were tested at various doses in mantle cell lymphoma (MCL) lines MAVER1, JVM2, Granta519, Mino, and Z138 for their effects on target knockdown and on cell line proliferation.
  • Target Knockdown
  • Cells were plated at a density of 10,000 cells per well and transfected by free uptake with 40 nM, 200 nM, 1,000 nM, or 5,000 nM concentrations of modified oligonucleotide, as specified in the tables below. Control oligonucleotide 549148, a 3-10-3 cEt gapmer with the sequence GGCTACTACGCCGTCA (SEQ ID NO: 3385), was also included. After a treatment period of approximately 48 hours, RNA was isolated from the cells and IRF4 mRNA levels were measured by RT-qPCR. Human IRF4 primer probe set RTS4522 (described hereinabove in Example 11) was used to measure mRNA levels. IRF4 mRNA levels were adjusted according to total RNA content, as measured by RiboGreen. Results are presented as the percent level of IRF4 mRNA transcript, relative to untreated control (UTC) cells. As illustrated in the tables below, IRF4 mRNA levels were reduced in a dose-dependent manner in cells treated with modified oligonucleotides.
  • TABLE 131
    Dose-dependent reduction of IRF4 expression
    by modified oligonucleotides in MAVER1 cells
    Compound IRF4 expression (% UTC)
    Number 40 nM 200 nM 1,000 nM 5,000 nM
    549148 115 103 96 99
    609408 121 102 80 35
    609416 108 109 87 65
  • TABLE 132
    Dose-dependent reduction of IRF4 expression
    by modified oligonucleotides in JVM2 cells
    Compound IRF4 expression (% UTC)
    Number 40 nM 200 nM 1,000 nM 5,000 nM
    549148 108 114 108 100
    609408 90 72 66 39
    609416 101 82 74 93
  • TABLE 133
    Dose-dependent reduction of IRF4 expression by
    modified oligonucleotides in Granta519 cells
    Compound IRF4 expression (% UTC)
    Number 40 nM 200 nM 1,000 nM 5,000 nM
    549148 106 95 95 65
    609408 176 165 134 122
    609416 119 168 130 97
    690890 161 160 143 102
  • TABLE 134
    Dose-dependent reduction of IRF4 expression
    by modified oligonucleotides in Mino cells
    Compound IRF4 expression (% UTC)
    Number 40 nM 200 nM 1,000 nM 5,000 nM
    549148 123 116 112 78
    609408 124 109 67 31
    609416 123 119 113 92
    690890 122 116 103 42
  • TABLE 135
    Dose-dependent reduction of IRF4 expression
    by modified oligonucleotides in Z138 cells
    Compound IRF4 expression (% UTC)
    Number 40 nM 200 nM 1,000 nM 5,000 nM
    549148 68 72 78 19
    609408 67 69 78 59
    609416 76 69 89 72
    690890 69 67 78 28
  • Proliferation
  • Cells were plated at a density of 2,000 cells per well and transfected by free uptake with 50 nM, 200 nM, 1,000 nM, or 5,000 nM concentrations of modified oligonucleotide, as specified in the tables below. After seven days, CellTiterGlo-2.0 (Promega) was added and luminescence was measured on Glomax (Promega).
  • TABLE 136
    Dose-dependent reduction of proliferation of
    MAVER1 cells by modified oligonucleotides
    Compound IRF4 proliferation (% UTC)
    Number 80 nM 400 nM 2,000 nM 10,000 nM
    549148 108 103 104 102
    609408 104 102 83 40
    609416 106 100 94 60
  • TABLE 137
    Dose-dependent reduction of proliferation
    of JVM2 cells by modified oligonucleotides
    Compound IRF4 proliferation (% UTC)
    Number 80 nM 400 nM 2,000 nM 10,000 nM
    549148 108 114 108 100
    609408 117 95 66 37
    609416 114 101 97 86
  • TABLE 138
    Dose-dependent reduction of proliferation of
    Granta519 cells by modified oligonucleotides
    Compound IRF4 proliferation (% UTC)
    Number 80 nM 400 nM 2,000 nM 10,000 nM
    549148 110 99 95 106
    609408 34 10 4 2
    609416 85 44 19 9
    690890 58 24 12 7
  • TABLE 139
    Dose-dependent reduction of proliferation
    of Mino cells by modified oligonucleotides
    Compound IRF4 proliferation (% UTC)
    Number 80 nM 400 nM 2,000 nM 10,000 nM
    549148 90 103 106 101
    609408 93 82 54 22
    609416 94 84 68 56
    690890 88 77 68 49
  • TABLE 140
    Dose-dependent reduction of proliferation
    of Z138 cells by modified oligonucleotides
    Compound IRF4 proliferation (% UTC)
    Number 80 nM 400 nM 2,000 nM 10,000 nM
    549148 91 88 89 82
    609408 98 83 70 46
    609416 91 82 74 56
    690890 95 84 74 50
  • Example 28: In Vivo Activity in MM1.R Xenograft Model
  • A xenograft MM1.R model was used to evaluate activity of modified oligonucleotides targeted to human IRF4. Female NOD/SCID mice (JAX) at 4-6 weeks of age were given a subcuntaneous injection of 6 million MM1.R cells to form a xenograft tumor. Two weeks later, groups of 3 mice were administered 25, 50, or 100 mg/kg/dose modified oligonucleotide once a day for three days by subcutaneous injection. One group of mice received subcutaneous injections of PBS once a day for three days. The saline-injected group served as the control group to which oligonucleotide-treated groups were compared. Mice were sacrificed 48 hours after the final dose and tumors were collected for further analysis.
  • RNA Analysis
  • RNA was extracted from tumor tissue for RT-PCR analysis, which was performed as described above. Data were analyzed with primer probe set 34726, described above in Example 7 or primer probe set 35624 (forward sequence TCCCGTGTTGCTTCAAACT, designated herein as SEQ ID NO: 3395; reverse sequence TACCTGCTGGCAGTTCTTTC, designated herein as SEQ ID NO: 3396; probe sequence ACAGATGGGACTTAACAGGCAATGGG, designated herein as SEQ ID: 3397), which specifically detect human IRF4, as indicated in the tables below. Results are presented as percent change of mRNA, relative to PBS control, normalized with human B-Actin levels from the human tumor cells and mouse stromal cells using human specific primer probe set 5002 (forward sequence CGGACTATGACTTAGTTGCGTTAC; designated herein as SEQ ID NO: 3398; reverse sequence GCCATGCCAATCTCATCTTGT, designated herein as SEQ ID NO: 3399; probe sequence CCTTTCTTGACAAAACCTAACTTGCGCAGA, designated herein as SEQ ID NO: 3400).
  • TABLE 141
    Activity of modified oligonucleotides in MM1.R xenograft model
    Compound IRF4 mRNA
    ID Dose PPset (% PBS)
    PBS n/a 34726 100
    690890 25 34726 59
    50 34726 53
    100 34726 24
    882800 50 34726 43
    100 34726 18
    935658 50 34726 52
    100 34726 22
    935918 50 34726 39
    100 34726 18
    935968 50 34726 52
    100 34726 22
    1012795 50 34726 45
    100 34726 26
    1014095 50 34726 71
    100 34726 34
    1014834 50 34726 56
    100 34726 32
    935762 50 34726 31
    100 34726 27
  • TABLE 142
    Activity of modified oligonucleotides in MM1.R xenograft model
    PBS n/a 34726 100
    935696 50 34726 28
    100 34726 13
  • TABLE 143
    Activity of modified oligonucleotides in MM1.R xenograft model
    Compound IRF4 mRNA
    ID Dose Ppset (% PBS)
    PBS n/a 35624 100
    690890 50 35624 55
    100 35624 33
    882800 50 35624 51
    100 35624 31
    935658 50 35624 56
    100 35624 27
    935918 50 35624 39
    100 35624 9.9
    935968 50 35624 26
    100 35624 9.1
    1012795 50 35624 18
    100 35624 21
    1014095 50 35624 28
    100 35624 27
    1014834 50 35624 33
    100 35624 15
    935762 50 35624 37
    100 35624 22
    935696 50 35624 19
    100 35624 15
  • Protein Analysis
  • Levels of hIRF4 protein were measured in the xenograft tumors by a human-specific IRF4 antibody (abeam EP5699) on the WES system (ProteinSimple).
  • Levels of Igλ, a clinically-relevant biomarker for MM, were also measured on the WES system. Reductions of hIRF4 and Igλ were observed.
  • TABLE 144
    Protein Levels in MM1.R Xenografts
    Compound Dose IRF4 Protein Igλ Protein
    ID (mg/kg/day) (% PBS) (% PBS)
    PBS n/a 100 100
    690890 50 53 83
    100 28 64
    882800 50 67 88
    100 27 68
    935918 50 41 103
    100 17 57
    935968 50 36 91
    100 15 52
    1012795 50 32 105
    100 14 60
    1014095 50 35 78
    100 15 56
    1014834 50 57 83
    100 31 69
    935762 50 46 69
    100 22 54
    935696 50 26 40
    100 15 37
    935658 50 45 102
    100 24 80
  • Example 29: Anti-Tumor Activity of Modified Oligonucleotides in a MM1.R Xenograft Model
  • A xenograft MM1.R model was used to evaluate activity of modified oligonucleotides targeted to human IRF4. Female NOD-SCID mice at 5-6 weeks of age were given a subcuntaneous injection of 3 million MM1.R cells to form a xenograft tumor. 23 days later, groups of 8 mice were administered 50 mg/kg/dose modified oligonucleotide five times a week by subcutaneous injection for 3.5 weeks. One group of mice received subcutaneous injections of PBS five times a week. The saline-injected group served as the control group to which oligonucleotide-treated groups were compared. Tumor volume was estimated by caliper measurement. Mice were sacrificed 24 hours after the last dose and tissue was collected for RNA and protein analysis.
  • Tumor Volume
  • TABLE 145
    Tumor volume (mm3)
    Compound Days after MM1.R Cell Injection
    ID 23 27 30 34 37 41 44
    PBS 215 374 590 936 1597  1877*  2530*
    792169 228 400 615 1194  1451  1669*  2394*
    1014834 225 319 451 606 931 1202  1733 
    1014095 222 291 504 554 886 795*  932*
    1012795 221 355 459 472  610* n.d. n.d.
    935968 210 313 463 587 771 447*  585*
    935918 219 346 569 705 899 746* 1024*
    935696 219 357 422 422 379 364  426
    935658 269 340 557 619 856 983  1299 
    935762 220 290 397  488*  593* 770*  949*
    882800 218 394 520 735 1075  907* 1279*
    690890 216 307 419 498 643 830  1191 
    *Values represent the average of 3-7 mice
  • Body Weight
  • Body weights were measured throughout the study as a measure of tolerability.
  • TABLE 146
    Body Weight (% of Day 23)
    Compound Days after MM1.R Cell Injection
    ID 23 27 30 34 37 41 44
    PBS 100 101 101 106 104* 111* 115*
    792169 100 106 106 116 121* 121* 126*
    1014834 100 102 101 103 107  107  108 
    1014095 100 100 98 98  98*  98*  95*
    1012795 100 101 97 82 n.d. n.d. n.d.
    935968 100 102 101 103 102* 102* 101*
    935918 100 101 101 102 100* 100*  98*
    935762 100 102 99 103 104  104  100 
    935696 100 104 103 105 101  101  97
    935658 100 100 100 100 98 98 95
    882800 100 102 101 106 103* 103*  98*
    690890 100 100 97 96 93 93 94
    *Values represent the average of 3-7 animals
  • Liver Function
  • To evaluate the effect of modified oligonucleotides on hepatic function, plasma levels of transaminases were measured using an automated clinical chemistry analyzer (Hitachi Olympus AU400e, Melville, N.Y.). Plasma levels of ALT (alanine transaminase) were measured and the results are presented in the table below expressed in IU/L.
  • TABLE 147
    Liver Transaminases
    Compound ID ALT (IU/L)
    PBS 24
    792169 45
    1014834 894
    1014095 1601
    1012795 1915
    935968 289
    935918 192
    935762 1016
    935696 1334
    935658 91
    882800 5219
    690890 496
  • RNA and Protein Analysis
  • IRF4 mRNA in tumor samples was measured by RT-PCR using PPset RTS34726, described above. IRF4 protein in tumor samples was determined by western blot as described in Example 28 above.
  • TABLE 148
    IRF4 Protein and mRNA Levels
    hIRF4 mRNA Level hIRF4 Protein Level
    PBS 98 100
    792169 159 110
    1014834 53 39
    1014095 58 43
    1012795 37 n.d.
    935968 41 35
    935918 28 31
    935762 47 34
    935696 39 27
    935658 51 43
    882800 57 32
    690890 49 46
  • Example 30: Efficacy of modified oligonucleotides targeted to hIRF4 in a Systemically Disseminated MM1.R Model with Bone Marrow Involvement
  • A systemically disseminated MM1.R model was used to evaluate activity of modified oligonucleotides targeted to human IRF4. Female nod-scid IL2Rγnull mice at 4-6 weeks of age were first administered 50 mg/kg cyclophosphamide on day 0, and on day 1 were administrated 10 million MM1.R cells via an intravenous injection. On day 14, plasma human Igλ was tested by ELISA and mice were randomized to groups based on these results. Starting on day 21, groups of 4 mice were administered 50 mg/kg/day modified oligonucleotide once a day for three days, and sacrificed 48 hours after the last dose. Levels of hIRF4 mRNA were measured in bone marrow. The tumor burden was measured by measuring levels of hActin mRNA. Results are presented as percent change of mRNA, relative to PBS control treated mice.
  • TABLE 149
    Bone marrow IRF4 mRNA and Tumor Burden.
    Compound IRF4 mRNA in bone marrow Tumor
    ID (% PBS) Burden
    PBS 100  4276
    792169 70  830
    882800 24  33
    935918 36* 118
    935696 38* 559
    935968 34* 18
    *Values represent the average of 1-3 mice, excluding mice with undetectable hIRF mRNA levels in bone marrow.
  • Example 31: Efficacy of Modified Oligonucleotides Targeted to hIRF4 in a Systemically Disseminated MM1.R Model with Bone Marrow Involvement
  • A systemically disseminated MM1.R model was used to evaluate activity of modified oligonucleotides targeted to human IRF4. Female NOD-SCID IL2Rγnull mice at 4-6 weeks of age were first administered 50 mg/kg cyclophosphamide on day 0, and on day 1 were administrated 10 million MM1.R cells via an intravenous injection. On day 14, serum human Igλ was tested by ELISA and mice were randomized to groups based on these results. Starting on day 15, groups of ten mice were administered modified oligonucleotide with a loading dose of 50 mg/kg/day for 1 week, and then 3 doses a week at 50 mg/kg/day continuing until animal death, bodyweight drop of <20% or paralysis. One group often mice was administered PBS as a control, and another group was administered the control oligonucleotide 792169.
  • TABLE 150
    Survival Percentage
    Treatment Compound ID
    Day PBS 792169 882800 935918 935696 935968
    0 100 100 100 100 100 100
    40 90 60 100 100 100 100
    42 90 60 90 100 90 100
    43 60 60 90 100 90 100
    44 40 20 90 100 90 100
    45 20 0 90 100 80 100
    46 0 0 90 100 80 100
    49 0 0 70 90 80 100
    51 0 0 70 90 80 100
  • Example 32: Activity of Modified Oligonucleotides Targeting hIRF4 in a TMD8 Human ABC-DLBCL Tumor Model
  • A xenograft tumor model was used to evaluate activity of modified oligonucleotides targeted to human IRF4. 4 million ABC-DLBCL TMD8 cells were implanted into the flanks of 5 week old female NOD/SCID mice. When tumors reached an average volume of 100 mm3, approximately two weeks post-implantation, groups of eight mice mice were administered 50 mg/kg/day modified oligonucleotide for two weeks. Mice were sacrificed after the last dose and tumors were collected for mRNA analysis.
  • Tumor volume was estimated with caliper measurement. Levels of hIRF4 mRNA were measured in tumor tissue and normalized to control animals.
  • TABLE 151
    Tumor volume (mm3)
    Days post-implantation
    Compound 15 19 22 25 27 29 32
    ID Tumor Volume (mm3)
    PBS 112 276 602 872 1162 1365 2012
    792169 112 232 488 797 1044 1359 1850
    690890 114 206 392 481 589 675 777
    882800 113 227 417 603 712 729 860
    935696 113 225 448 570 676 761 729
  • TABLE 152
    hIRF4 mRNA levels
    hIRF4 mRNA Level
    PBS 100
    792169 127
    690890 84
    882800 72
    935696 58
  • Example 33: Tolerability of Modified Oligonucleotides Targeting hIRF4 in Balb/c Mice
  • Balb/c mice are frequently utilized for safety and efficacy testing. The mice were treated with antisense oligonucleotides selected from studies described above and evaluated for changes in the levels of various plasma chemistry markers.
  • Treatment
  • Groups of 4-6 week old male Balb/c mice were injected subcutaneously twice a week for four weeks with 50 mg/kg of modified oligonucleotides (100 mg/kg/week dose). One group of male Balb/c mice was injected subcutaneously twice a week for 4 weeks with PBS. Mice were euthanized 48 hours after the last dose, and organs and plasma were harvested for further analysis.
  • Plasma Chemistry Markers
  • To evaluate the effect of modified oligonucleotides on liver and kidney function, plasma levels of transaminases, bilirubin, and BUN were measured using an automated clinical chemistry analyzer (Hitachi Olympus AU400e, Melville, N.Y.). The results are presented in the table below. Modified oligonucleotides that caused changes in the levels of any of the liver or kidney function markers outside the expected range for modified oligonucleotides were excluded in further studies.
  • TABLE 153
    Plasma chemistry markers in Balb/c mouse plasma at week 4
    Compound ALT AST BUN T. Bil
    ID (U/L) (U/L) (mg/dL) (mg/dL)
    PBS 37  84 22.9 0.25
    609296 n.d. n.d. n.d. n.d.
    609343 n.d. n.d. n.d. n.d.
    609354 n.d. n.d. n.d. n.d.
    609357 n.d. n.d. n.d. n.d.
    609391 1799  1362  16.7 0.31
    609408 859  507 18.4 0.28
    609416 93 114 21.1 0.23
    609296 n.d. n.d. n.d. n.d.
    609547 982  802 27.3 0.34
    609592 53 170 21.2 0.25
  • TABLE 154
    Plasma chemistry markers in Balb/c mouse plasma at week 4
    Compound ALT AST BUN T. Bil
    ID (U/L) (U/L) (mg/dL) (mg/dL)
    PBS 35.8 53 21.1 0.25
    666431 85.5 120 21.1 0.29
    666440 8173 3432 26.2 3.84
    666449 150 124 24.9 0.18
    666471 n.d. n.d. n.d. n.d.
    666475 1989 1607 25.0 0.23
    666496 2926 2423 22.4 0.30
    666569 3427 3288 23.8 0.23
    666575 525 385 24.5 0.21
    666582 3543 2893 20.0 0.44
    666584 43.3 57 25.4 0.21
    666586 2970 2051 23.8 0.26
    666587 1057 964 28.1 0.16
    666649 4662 3970 23.8 10.99 
    666683 1363 1657 21.3 0.19
  • TABLE 155
    Plasma chemistry markers in Balb/c mouse plasma at week 4
    Compound ALT AST BUN T. Bil
    ID (U/L) (U/L) (mg/dL) (mg/dL)
    PBS  32  89 24.1 0.29
    609555 737 238 25.9 0.15
    666772 n.d. n.d. n.d. n.d
    666775 n.d. n.d. n.d. n.d
    668818 n.d. n.d. n.d. n.d
    668849 105 131 24.7 0.12
    668850 547 394 27.8 0.11
    668902  53 103 21.5 0.18
    668934 n.d. n.d. n.d. n.d
    668936 2260  3211  24.8 0.13
    668937  39  89 23.2 0.14
    668947 n.d. n.d. n.d. n.d
    668998 102 101 21.7 0.14
    668999 625 404 28.9 0.21
    669018 198 157 28.1 0.17
    669022  33  60 19.9 0.19
    669040 176 170 23.2 0.11
    669066 589 300 23.8 0.27
    669067 n.d. n.d. n.d. n.d
    669068  95 137 20.0 0.16
    669075 647 400 19.4 0.15
  • TABLE 156
    Plasma chemistry markers in Balb/c mouse plasma at week 4
    Compound ALT AST BUN T. Bil
    ID (U/L) (U/L) (mg/dL) (mg/dL)
    PBS  21  77 22.8 0.16
    690508 n.d. n.d. n.d. n.d.
    690509 n.d. n.d. n.d. n.d.
    690510 n.d. n.d. n.d. n.d.
    690511 n.d. n.d. n.d. n.d.
    690512 n.d. n.d. n.d. n.d.
    690514 595 440 19.3 0.15
    690515 n.d. n.d. n.d. n.d.
    690522 2440  1878  26.6 0.23
    690527 n.d. n.d. n.d. n.d.
    690861 933 752 12.2 0.19
    690863 889 798 17.0 0.56
    690865 n.d. n.d. n.d. n.d.
    690873 1844  1160  16.6 0.28
    690875 887 770 16.3 0.16
    690877 n.d. n.d. n.d. n.d.
    690879 887 652 22.2 0.21
    690881 442 320 23.0 0.12
    690883 1505  901 38.9 0.34
    690890  76  64 25.6 0.14
    690892  56 126 23.9 0.17
    690898  47 120 27.4 0.11
    691028 n.d. n.d. n.d. n.d.
    691032 588 216 216   0.16
    691033 709 451 31.4 0.13
  • Organ Weights
  • Liver, kidney, and spleen weights were measured at the end of the study, and are presented as the percent change compared to PBS-treated animals in the table below. Modified oligonucleotides that caused any changes in organ weights outside the expected range for modified oligonucleotides were excluded from further studies.
  • TABLE 157
    Organ Weights (g)
    Compound ID Liver Kidney Spleen
    PBS 1.25 0.39 0.11
    609296 n.d. n.d. n.d.
    609343 n.d. n.d. n.d.
    609354 n.d. n.d. n.d.
    609357 n.d. n.d. n.d.
    609391 1.29 0.32 0.23
    609408 1.48 0.37 0.14
    609416 1.57 0.38 0.14
    609296 n.d. n.d. n.d.
    609547 2.56 0.35 0.55
    609592 1.41 0.37 0.13
  • TABLE 158
    Organ Weights (g)
    Compound ID Liver Kidney Spleen
    PBS 1.30 0.40 0.10
    666431 1.21 0.38 0.15
    666440 2.38 0.37 0.10
    666449 1.39 0.40 0.11
    666471 n.d. n.d. n.d.
    666475 1.49 0.40 0.10
    666496 1.66 0.44 0.12
    666569 1.09 0.34 0.13
    666575 1.33 0.37 0.10
    666582 2.03 0.42 0.13
    666584 1.34 0.40 0.11
    666586 1.36 0.29 0.12
    666587 1.77 0.38 0.11
    666649 0.81 0.30 0.07
    666683 2.05 0.38 0.12
  • TABLE 159
    Organ weights (g)
    Compound ID Liver (g) Kidney (g) Spleen (g)
    PBS 1.49 0.43 0.12
    609555 1.50 0.36 0.17
    666772 n.d. n.d. n.d.
    666775 n.d. n.d. n.d.
    668818 n.d. n.d. n.d.
    668849 1.75 0.41 0.22
    668850 1.96 0.41 0.16
    668902 1.50 0.39 0.12
    668934 n.d. n.d. n.d.
    668936 1.97 0.33 0.13
    668937 1.58 0.41 0.14
    668947 n.d. n.d. n.d.
    668998 1.53 0.38 0.16
    668999 1.64 0.38 0.13
    669018 1.92 0.41 0.14
    669022 1.47 0.41 0.12
    669040 1.66 0.44 0.11
    669066 1.64 0.39 0.15
    669067 1.52 0.38 0.13
    669068 n.d. n.d. n.d.
    669075 1.43 0.36 0.17
  • TABLE 160
    Organ weights (g)
    Compound ID Liver (g) Kidney (g) Spleen (g)
    PBS 0.86 0.29 0.10
    690508 n.d. n.d. n.d.
    690509 n.d. n.d. n.d.
    690510 n.d. n.d. n.d.
    690511 n.d. n.d. n.d.
    690512 n.d. n.d. n.d.
    690514 1.68 0.28 0.19
    690515 n.d. n.d. n.d.
    690522 1.40 0.26 0.11
    690527 n.d. n.d. n.d.
    690861 1.29 0.27 0.12
    690863 1.27 0.27 0.15
    690865 n.d. n.d. n.d.
    690873 1.17 0.28 0.14
    690875 1.36 0.28 0.17
    690877 n.d. n.d. n.d.
    690879 1.04 0.26 0.14
    690881 1.19 0.28 0.13
    690883 1.59 0.30 0.10
    690890 0.97 0.27 0.13
    690892 1.08 0.30 0.17
    690898 1.08 0.30 0.15
    691028 n.d. n.d. n.d.
    691032 1.33 0.29  0.1525
    691033  1.625  0.3175  0.125
  • Example 34: Tolerability of Modified Oligonucleotides Targeting hIRF4 in CD1 Mice
  • CD1® mice (Charles River, Mass.) are frequently utilized for safety and efficacy testing. The mice were treated with antisense oligonucleotides selected from studies described above and evaluated for changes in the levels of various plasma chemistry markers.
  • Treatment
  • Groups of 4-6 week old male CD1 mice were injected subcutaneously twice a week for four weeks with 50 mg/kg of modified oligonucleotides (100 mg/kg/week dose). One group of male CD1 mice was injected subcutaneously twice a week for 4 weeks with PBS. Mice were euthanized 48 hours after the last dose, and organs and plasma were harvested for further analysis.
  • Plasma Chemistry Markers
  • To evaluate the effect of modified oligonucleotides on liver and kidney function, plasma levels of transaminases, bilirubin, and BUN were measured using an automated clinical chemistry analyzer (Hitachi Olympus AU400e, Melville, N.Y.). The results are presented in the table below. Modified oligonucleotides that caused changes in the levels of any of the liver or kidney function markers outside the expected range for modified oligonucleotides were excluded in further studies.
  • TABLE 161
    Plasma chemistry markers in CD1 mouse plasma at week 4
    Compound ALT AST BUN T. Bil
    ID (U/L) (U/L) (mg/dL) (mg/dL)
    PBS 27 65 19.7 0.19
    881413 43 78 19.3 0.18
    881442 594 484 23.1 0.24
    881449 36 52 19.9 0.24
    881450 100 146 20.8 0.18
    881506 683 417  8.7 0.18
    881517 121 103 22.1 0.16
    881581 501 413 23.7 0.27
    881610 44 79 18.5 0.19
    881658 39 66 16.0 0.17
    881659 4924 3485 15.3 5.48
    881660 267 176 19.7 0.16
    881728 644 389 21.1 0.23
    881742 780 443 17.6 0.23
    882099 3607 1971 23.1 0.28
    882282 n.d. n.d. n.d. n.d.
    882305 2688 1379 24.9 0.31
    882433 2683 1944 19.5 0.42
  • TABLE 162
    Plasma chemistry markers in CD1 mouse plasma at week 4
    Compound ALT AST BUN T. Bil
    ID (U/L) (U/L) (mg/dL) (mg/dL)
    PBS 23 69 17.0 0.19
    881449 34 65 19.2 0.23
    881582 206 211 18.6 0.15
    881588 902 829 15.2 0.32
    881658 334 226 14.0 0.18
    881727 1120 748 16.8 0.40
    792169 23 43 18.0 0.21
  • TABLE 163
    Plasma chemistry markers in CD1 mouse plasma at week 4
    Compound ALT AST BUN T. Bil
    ID (U/L) (U/L) (mg/dL) (mg/dL)
    PBS 25  41 22.2 0.17
    935765 n.d. n.d. n.d. n.d.
    935580 n.d. n.d. n.d. n.d.
    935805 n.d. n.d. n.d. n.d.
    935853 n.d. n.d. n.d. n.d.
    935824 n.d. n.d. n.d. n.d.
    935581 n.d. n.d. n.d. n.d.
    935689 n.d. n.d. n.d. n.d.
    935698 1462 1523  17.5 0.19
    935699 n.d. n.d. n.d. n.d.
    935707 1334 703 17.3 0.21
    935679 n.d. n.d. n.d. n.d.
    935727 n.d. n.d. n.d. n.d.
    935795 n.d. n.d. n.d. n.d.
    935898 101 129 20.3 0.18
    935782 680 278 19.0 0.20
    935878 1805 1128  19.1 0.21
    935850 661 492 21.2 0.08
    935724 1630 1341  19.9 0.25
    935658 53  65 19.5 0.24
    935762 106 132 18.0 0.18
    935851 513 300 18.0 0.13
  • TABLE 164
    Plasma chemistry markers in CD1 mouse plasma at week 4
    Compound ALT AST BUN T. Bil
    ID (U/L) (U/L) (mg/dL) (mg/dL)
    PBS 19 34 18.6 0.17
    935921 708 372 15.5 0.19
    935961 1068 754 14.8 0.28
    936018 609 358 17.9 0.14
    936039 n.d. n.d. n.d. n.d.
    935708 n.d. n.d. n.d. n.d.
    935958 97 117 17.5 0.10
    935854 304 205 18.6 0.14
    935968 53 70 18.9 0.12
    935620 1883 2950 17.2 1.17
    935697 1504 763 16.9 0.22
    935700 722 480 18.8 0.18
    935734 1253 500 17.9 0.17
    935857 1270 1233 17.7 0.29
    936016 731 571 22.7 0.15
    936006 38 47 16.9 0.13
    936007 131 152 18.1 0.10
    935948 192 183 19.5 0.15
    935603 193 260 17.0 0.19
    935701 426 277 18.0 0.06
    935928 69 84 17.4 0.10
  • TABLE 165
    Plasma chemistry markers in CD1 mouse plasma at week 4
    Compound ALT AST BUN T. Bil
    ID (U/L) (U/L) (mg/dL) (mg/dL)
    PBS 23 44 22.5 0.20
    969991 n.d. n.d. n.d. n.d.
    970013 n.d. n.d. n.d. n.d.
    970043 636 610 19.6 0.33
    970103 786 512 20.1 0.17
    970117 1786 877 22.5 0.29
    970139 1011 1244 21.0 1.69
    970159 1772 3821 15.7 2.68
    970162 470 422 18.0 0.15
    970189 353 377 21.0 0.19
    970212 1714 1062 22.7 1.00
    970524 n.d. n.d. n.d. n.d.
    970527 182 181 18.1 0.12
  • TABLE 166
    Plasma chemistry markers in CD1 mouse plasma at week 4
    Compound ALT AST BUN T. Bil
    ID (U/L) (U/L) (mg/dL) (mg/dL)
    PBS 24 99 20.1 0.21
    881955 4127 3743 45.7 2.61
    882085 53 73 22.3 0.18
    882086 2522 2002 25.5 0.43
    882087 377 276 23.1 0.15
    882175 575 554  9.4 0.68
    882177 2666 3030 26.6 4.87
    882228 893 1659 19.3 0.22
    882398 980 1070 22.1 7.91
    882408 46 69 17.9 0.17
    882800 70 84 23.4 0.20
    969933 383 272 21.7 0.15
    969936 n.d. n.d. n.d. n.d.
    969938 1142 1009 18.1 0.76
    970211 301 224 20.1 0.15
    970249 1724 2104 20.0 6.21
    970545 836 1049 24.8 0.34
    970546 1248 1334 23.8 0.31
    970547 878 665 18.4 0.53
    970548 1607 3352 17.7 4.86
    970552 n.d. n.d. n.d. n.d.
  • TABLE 167
    Plasma chemistry markers in CD1 mouse plasma at week 4
    Compound ALT AST BUN T. Bil
    ID (U/L) (U/L) (mg/dL) (mg/dL)
    PBS 23 44 19.7 0.22
    1012795 143 235 20.9 0.16
    1012821 1189 1434 24.6 0.22
    1012884 1523 1939 27.0 0.69
    1014095 63 71 19.4 0.18
    1014393 666 627 19.3 0.25
    1014394 117 129 17.8 0.16
    1014834 301 190 19.7 0.21
    1015716 230 205 18.4 0.17
  • TABLE 168
    Plasma chemistry markers in CD1 mice plasma at week 4
    Compound ALT AST T. Bil BUN
    ID (U/L) (U/L) (mg/dL) (mg/dL) Albumin
    PBS 21 45 0.190 21.8 2.54
    935918 87 91 0.118 18.8 2.07
    935696 71 108 0.143 21.7 2.22
  • Organ Weights
  • Liver, kidney, and spleen weights were measured at the end of the study, and are presented as the percent change compared to PBS-treated animals in the table below. Modified oligonucleotides that caused any changes in organ weights outside the expected range for modified oligonucleotides were excluded from further studies.
  • TABLE 169
    Organ Weights (g)
    Compound ID Liver Kidney Spleen
    PBS 2.1 0.56 0.141
    881413 2.2 0.57 0.217
    881442 2.7 0.52 0.186
    881449 2.1 0.47 0.169
    881450 2.2 0.50 0.151
    881506 2.9 0.62 0.191
    881517 2.4 0.48 0.180
    881581 2.2 0.51 0.192
    881610 1.9 0.53 0.165
    881658 2.0 0.54 0.158
    881659 1.7 0.43 0.153
    881660 1.9 0.52 0.175
    881728 2.3 0.48 0.161
    881742 1.9 0.48 0.127
    882099 2.2 0.47 0.193
    882282 n.d. n.d. n.d.
    882305 2.1 0.52 0.181
    882433 2.0 0.54 0.155
  • TABLE 170
    Organ weights (g)
    Compound ID Liver Kidney Spleen
    PBS 1.8 0.54 0.111
    881449 2.1 0.54 0.146
    881582 2.0 0.48 0.177
    881588 1.9 0.39 0.171
    881658 2.2 0.58 0.188
    881727 2.1 0.51 0.201
    792169 1.9 0.55 0.128
    UTC 2.0 0.69 0.144
  • TABLE 171
    Organ weights (g)
    Compound ID Liver Kidney Spleen
    PBS 2.0 0.50 0.109
    935765 n.d. n.d. n.d.
    935580 n.d. n.d. n.d.
    935805 n.d. n.d. n.d.
    935853 n.d. n.d. n.d.
    935824 n.d. n.d. n.d.
    935581 n.d. n.d. n.d.
    935689 n.d. n.d. n.d.
    935698 2.4 0.55 0.213
    935699 n.d. n.d. n.d.
    935707 2.3 0.54 0.199
    935679 n.d. n.d. n.d.
    935727 n.d. n.d. n.d.
    935795 n.d. n.d. n.d.
    935898 2.2 0.58 0.245
    935782 2.9 0.56 0.279
    935878 2.7 0.56 0.192
    935850 2.8 0.70 0.203
    935724 2.6 0.45 0.110
    935658 2.0 0.71 0.205
    935762 2.3 0.57 0.197
    935851 2.4 0.60 0.176
  • TABLE 172
    Organ weights (g)
    Compound ID Liver Kidney Spleen
    PBS 1.9 0.52 0.117
    935921 2.3 0.51 0.219
    935961 2.1 0.53 0.190
    936018 2.2 0.41 0.200
    936039 n.d. n.d. n.d.
    935708 n.d. n.d. n.d.
    935958 2.2 0.47 0.219
    935854 2.0 0.44 0.102
    935968 2.4 0.58 0.157
    935620 3.2 0.57 0.243
    935697 2.9 0.56 0.208
    935700 2.0 0.49 0.121
    935734 2.7 0.55 0.162
    935857 1.5 0.34 0.110
    936016 2.8 0.57 0.416
    936006 2.3 0.48 0.136
    936007 2.3 0.55 0.149
    935948 1.9 0.54 0.166
    935603 1.6 0.49 0.125
    935701 1.9 0.43 0.144
    935928 2.3 0.53 0.155
  • TABLE 173
    Organ weights (g)
    Compound ID Liver Kidney Spleen
    PBS 1.8 0.51 0.133
    969991 n.d. n.d. n.d.
    970013 n.d. n.d. n.d.
    970043 2.3 0.48 0.238
    970103 2.2 0.54 0.175
    970117 3.2 0.48 0.255
    970139 2.7 0.56 0.210
    970159 2.7 0.62 0.183
    970162 2.2 0.54 0.215
    970189 3.1 0.45 0.135
    970212 2.3 0.45 0.218
    970524 n.d. n.d. n.d.
    970527 2.4 0.60 0.178
  • TABLE 174
    Organ weights (g)
    Compound ID Liver Kidney Spleen
    PBS 1.7 0.42 0.095
    881955 1.8 0.32 0.110
    882085 2.0 0.45 0.110
    882086 4.9 0.41 0.258
    882087 2.4 0.47 0.130
    882175 1.4 0.46 0.098
    882177 3.6 0.43 0.185
    882228 2.8 0.49 0.193
    882398 1.7 0.44 0.113
    882408 2.0 0.51 0.135
    882800 1.9 0.41 0.128
    969933 2.2 0.50 0.145
    969936 n.d. n.d. n.d.
    969938 1.8 0.45 0.150
    970211 2.1 0.40 0.143
    970249 3.3 0.65 0.190
    970545 2.5 0.44 0.133
    970546 0.9 0.28 0.060
    970547 2.1 0.50 0.243
    970548 2.8 0.52 0.260
    970552 n.d. n.d. n.d.
  • TABLE 175
    Organ weights (g)
    Compound Liver Kidney Spleen
    PBS 1.78 0.56 0.115
    935918 2.44 0.62 0.167
    935696 2.20 0.61 0.352
  • Example 35: Tolerability of Modified Oligonucleotides Targeting hIRF4 in Sprague-Dawley Rats
  • Sprague-Dawley rats are a multipurpose model used for safety and efficacy evaluations. The rats were treated with modified antisense oligonucleotides from the studies described in the Examples above and evaluated for changes in the levels of various plasma chemistry markers.
  • Treatment
  • Male Sprague-Dawley rats were maintained on a 12-hour light/dark cycle and fed ad libitum with Purina normal rat chow, diet 5001. Groups of 4Sprague-Dawley rats each were injected subcutaneously once a week for 6 weeks with 50 mg/kg of ISIS oligonucleotide (50 mg/kg weekly dose). Forty eight hours after the last dose, rats were euthanized and organs and plasma were harvested for further analysis.
  • Liver and Kidney Function
  • To evaluate the effect of modified oligonucleotides on hepatic function, plasma levels of transaminases were measured using an automated clinical chemistry analyzer (Hitachi Olympus AU400e, Melville, N.Y.). Plasma levels of ALT (alanine transaminase), AST (aspartate transaminase), blood urea nitrogen (BUN), and T. bilirubin were measured and the results are presented in the table below. Plasma levels of bilirubin were also measured using the same clinical chemistry analyzer and the results are also presented in the table below. Values represent the % change normalized to PBS-treated animals. Modified oligonucleotides that caused changes in the levels of any markers of liver function outside the expected range for antisense oligonucleotides were excluded in further studies.
  • TABLE 176
    Liver function markers in Sprague-Dawley rats
    Compound ALT AST T. Bil BUN Albumin
    ID (IU/L) (IU/L) (mg/dL) (mg/dL) (g/dL)
    PBS 47 67 0.14 16.4 3.92
    690898 41 73 0.17 20.7 3.19
    881413 42 61 0.18 18.1 3.66
    881449 47 67 0.26 19.7 3.77
    935658 47 55 0.16 17.4 3.80
    935696 41 70 0.18 16.9 3.55
    935898 72 81 0.19 18.0 4.23
    935928 189 188 0.19 19.7 3.59
    935968 39 85 0.21 17.2 3.61
    936006 40 55 0.14 14.3 3.97
  • TABLE 177
    Liver function markers in Sprague-Dawley rats
    Compound ALT AST T. Bil BUN Albumin
    ID (IU/L) (IU/L) (mg/dL) (mg/dL) (g/dL)
    PBS 34 58 0.09 15.7 2.20
    690890 32 70 0.16 20.1 2.39
    690892 42 77 0.15 18.5 1.82
    882085 68 73 0.09 47.1 1.36
    882800 40 100 0.16 20.2 2.30
    970527 45 80 0.12 19.8 2.09
  • TABLE 178
    Liver function markers in Sprague-Dawley rats
    Compound ALT AST T. Bil BUN Albumin
    ID (IU/L) (IU/L) (mg/dL) (mg/dL) (g/dL)
    PBS 41 70 0.14 14.4 3.60
    882408 38 68 0.15 17.0 2.80
    1012795 25 70 0.09 22.3 2.47
    1014095 37 101 0.12 20.3 2.41
    1014393 41 70 0.09 20.3 2.28
    1014394 32 74 0.08 21.1 2.53
    1014834 34 68 0.10 14.2 3.04
  • TABLE 179
    Liver function markers in Sprague-Dawley rats
    Compound ALT AST T. Bil BUN Albumin
    ID (IU/L) (IU/L) (mg/dL) (mg/dL) (g/dL)
    PBS 55 51 0.15 17.1 3.04
    935762 35 53 0.14 18.7 2.63
    935918 31 55 0.15 19.7 2.60
  • Hematology Assays
  • Blood obtained from all rat groups were sent to Antech Diagnostics for hematocrit (HCT) measurements and analysis, as well as measurements of the various blood cells, such as WBC, RBC, and total hemoglobin content. The results are presented in the table below. Modified oligonucleotides that caused changes in the levels of any of the hematology markers outside the expected range for antisense oligonucleotides were excluded in further studies.
  • TABLE 180
    Hematology markers in Sprague-Dawley rats
    Compound WBC RBC HGB HCT LYM MON EOS BAS PLT Retic
    ID (K/μL) (M/μL) (g/dL) (%) (/μL) (/μL) (/μL) (/μL) (K/μL) (K/μL)
    PBS 10.38 8.15 14.80 43.9 8711 357 68.3 12.3 868 252
    690898 17.83 6.46 12.27 37.1 15745 1109 75.0 145.0 214 201
    881413 7.08 6.71 12.55 36.6 6342 286 44.3 15.3 523 152
    881449 6.68 7.53 13.60 39.8 5414 396 153.0 27.5 583 133
    935658 9.73 7.97 14.53 42.4 8250 777 19.7 70.0 685 138
    935696 7.80 7.33 13.10 38.6 6354 645 48.8 23.0 480 97
    935898 7.75 8.64 15.20 43.3 6248 529 29.3 26.8 712 114
    935928 13.15 7.36 13.23 40.1 7231 1177 8.5 90.3 476 160
    935968 6.15 6.17 11.28 33.7 5292 436 8.0 68.8 462 178
    936006 7.28 8.07 14.45 42.7 5875 729 20.3 57.3 621 220
  • TABLE 181
    Hematology markers in Sprague-Dawley rats
    Compound WBC RBC HGB HCT LYM MON EOS BAS PLT Retic
    ID (K/μL) (M/μL) (g/dL) (%) (/μL) (/μL) (/μL) (/μL) (K/μL) (K/μL)
    PBS 4.35 5.18 9.68 29.4 3546 116 102.8 10.5 292 136
    690890 4.75 4.84 8.98 27.4 3844 325 25.3 55.0 190 113
    690892 4.70 5.46 10.65 31.4 3917 276 42.3 34.5 184 120
    882085 7.18 5.18 9.43 29.2 5159 758 73.0 24.5 352 122
    882800 5.10 5.08 9.13 27.9 4190 479 46.0 40.3 165 157
    970527 9.60 6.10 10.88 32.4 7990 846 28.3 50.8 249 123
  • TABLE 182
    Hematology markers in Sprague-Dawley rats
    Compound WBC RBC HGB HCT LYM MON EOS BAS PLT Retic
    ID (K/μL) (M/μL) (g/dL) (%) (/μL) (/μL) (/μL) (/μL) (K/μL) (K/μL)
    PBS 9.35 7.81 14.28 46.6 7820 330 208.3 11.3 344 214
    882408 13.25 9.46 16.73 52.0 8387 1020 35.3 29.3 407 163
    1012795 15.20 4.86 10.03 33.6 11767 1996 28.5 12.8 149 304
    1014095 18.55 6.93 12.35 41.4 11958 1500 95.0 22.3 727 281
    1014393 21.90 7.25 13.08 41.8 17709 2038 50.5 156.3 491 123
    1014394 23.55 7.21 13.58 43.3 19656 2121 31.8 67.5 270 207
    1014834 14.43 7.97 14.65 45.9 12543 1009 42.3 180.0 395 182
  • TABLE 183
    Hematology markers in Sprague-Dawley rats
    Compound WBC RBC HGB HCT LYM MON EOS BAS PLT Retic
    ID (K/μL) (M/μL) (g/dL) (%) (/μL) (/μL) (/μL) (/μL) (K/μL) (K/μL)
    PBS 11.13 9.45 16.70 52.8 9156 686 103 8.0 82 238
    935762 14.53 7.72 13.43 42.4 13586 510 0 29.3 92 232
    935918 9.25 7.08 12.50 40.5 8509 456 51 5.0 92 286
  • Organ Weights
  • Liver, heart, spleen and kidney weights were measured at the end of the study, and are presented in the table below. Modified oligonucleotides that caused any changes in organ weights outside the expected range for antisense oligonucleotides were excluded from further studies.
  • TABLE 184
    Organ weights (g)
    Compound ID Liver (g) Kidney (g) Spleen (g)
    PBS 15.8 2.91 0.90
    690898 16.9 3.18 3.65
    881413 15.0 2.83 1.32
    881449 15.4 3.07 1.19
    935658 13.8 2.40 1.33
    935696 12.6 2.60 1.22
    935898 12.0 2.44 1.07
    935928 16.8 3.23 1.94
    935968 14.9 2.85 1.56
    936006 14.2 2.75 1.59
  • TABLE 185
    Organ weights (g)
    Compound ID Liver (g) Kidney (g) Spleen (g)
    PBS 15.2 3.38 0.72
    690890 15.8 3.17 1.62
    690892 15.2 3.27 1.72
    882085 12.5 3.78 1.41
    882800 17.0 3.46 3.24
    970527 14.0 3.72 1.94
  • TABLE 186
    Organ weights (g)
    Compound ID Liver (g) Kidney (g) Spleen (g)
    PBS 18.6 3.70 0.92
    882408 15.1 3.60 1.51
    1012795 18.9 3.70 4.06
    1014095 18.2 3.63 3.05
    1014393 15.9 3.98 2.30
    1014394 18.3 4.41 2.79
    1014834 14.4 3.35 5.01
  • TABLE 187
    Organ weights (g)
    Compound ID Liver (g) Kidney (g) Spleen (g)
    PBS 14.6 3.20 0.88
    935762 16.1 3.43 1.73
    935918 18.7 3.89 2.01
  • Example 36: Tolerability of Modified Oligonucleotides in Non-Human Primates
  • Modified oligonucleotides described above were further evaluated for potency in non-human primates.
  • Treatment
  • Male cynomolgus monkeys were divided into groups of 4 non-human primates (NHP) each. Groups received a dose of 40 mg/kg of modified oligonucleotide by subcutaneous injection on day 1, 3, 5, and 7, and then once/week for six weeks. One group of NHP received doses of PBS. The PBS-injected group served as the control group to which oligonucleotide-treated groups were compared. After six weeks, NHP were sacrificed and tissues were collected for analysis.
  • Tolerability
  • To evaluate the effect of these antisense oligonucleotides on liver and kidney function, samples of blood, plasma, serum and urine were collected from all study groups on day 44. The blood samples were collected via femoral venipuncture, 48 hrs post-dosing. The monkeys were fasted overnight prior to blood collection. Approximately 1.5 mL of blood was collected from each animal into tubes without anticoagulant for serum separation. Levels of the various markers were measured using an automated clinical chemistry analyzer (Hitachi Olympus AU400e, Melville, N.Y.). Total urine protein and urine creatinine levels were measured, and the ratio of total urine protein to creatinine (P/C Ratio) was determined.
  • To evaluate the effect of the antisense oligonucleotides on hepatic function, plasma concentrations of transaminases (ALT, AST), Albumin (Alb) and total bilirubin (“T. Bil”) were measured. To evaluate the effect of the antisense oligonucleotides on kidney function, plasma concentrations of blood urea nitrogen (BUN) and creatinine (Cre) were measured. Urine levels of albumin (Alb), creatinine (Cre) and total urine protein (Micro Total Protein (MTP)) were measured, and the ratio of total urine protein to creatinine (P/C ratio) was determined.
  • To evaluate any inflammatory effect of the ISIS oligonucleotides in cynomolgus monkeys, C-reactive protein (CRP), which is synthesized in the liver and which serves as a marker of inflammation, was measured on day 44. For this, blood samples were taken from fasted monkeys, the tubes were kept at room temperature for a minimum of 90 min., and centrifuged at 3,000 rpm for 10 min at room temperature to obtain serum. The results are presented in the Tables below and indicate that most of the antisense oligonucleotides targeting human IRF4 were well tolerated in cynomolgus monkeys. ION 935918 and 935968 were well tolerated.
  • TABLE 188
    Serum and urine clinical chemistry
    Serum (day 44) Urine (day 42)
    ISIS C3 ALT AST Alb BUN CRP Cre T. bil Alb Cre P/C
    No. mg/dL U/L U/L g/dL mg/dL mg/L mg/dL mg/dL g/dL mg/dL ratio
    PBS 120.73 48.00 69.10 4.35 25.60 1.66 0.858 0.29 0.35 55.0 0.00
    690890 71.20 50.18 75.20 3.66 26.10 9.52 0.988 0.23 0.53 56.2 0.04
    935658 95.90 42.33 81.85 3.99 21.70 4.53 0.808 0.29 0.68 39.0 0.12
    935696 88.58 48.32 62.78 4.03 26.06 6.55 0.780 0.26 0.18 36.6 0.04
    935762 100.10 47.58 52.63 3.91 24.98 6.88 0.76 0.25 0.03 37.9 0.01
    935918 94.45 49.45 79.20 4.05 29.85 4.65 0.90 0.24 0.12 60.2 0.01
    935968 108.83 54.45 83.33 4.10 28.68 6.65 0.813 0.23 0.10 38.8 0.07
    882800 100.83 46.55 61.80 4.00 24.10 2.53 0.818 0.22 0.36 34.9 0.14
    1012795 82.05 37.08 51.40 3.05 27.45 21.28 0.763 0.20 0.50 55.0 0.10
    1014095 85.83 38.15 46.85 2.81 15.10 11.16 0.593 0.15 0.03 43.9 0.07
    1014834 89.13 54.73 75.28 3.88 23.65 7.03 0.978 0.25 0.14 75.9 0.05
  • TABLE 189
    Body Weight
    Compound ID Body Weight (g) day 1 Body weight (g) day 42
    PBS 2521 2594
    690890 2508 2514
    935658 2499 2557
    935696 2412 2511
    935762 2473 2653
    935918 2483 2657
    935968 2605 2798
    882800 2577 2676
    1012795 2623 2577
    1014095 2567 2719
    1014834 2556 2685
  • RNA Analysis
  • RNA was extracted from various tissues for real-time PCR analysis of mRNA expression of IRF4 as in previous examples. Results are presented as percent change of mRNA, relative to PBS control, normalized with NHP Cyclophylin A. As shown in the table below, treatment with modified oligonucleotides resulted in reduction of IRF4 mRNA in comparison to the PBS control with some of the treatment groups.
  • TABLE 190
    % Inhibition of cynomolgus IRF4
    Compound ID Bone marrow PBMC Spleen
    PBS 100 100 100
    690890* 98 119 205
    935658* 174 170 200
    935696* 71 80 125
    935762* 112 90 129
    935918* 98 41 192
    935968* 129 49 131
     882800*** 107 75 133
    1012795*  97 95 151
     1014095*** 80 80 188
    1014834*  139 180 192
    *Compounds have one mismatch to cynomolgus monkey IRF4;
    ***compounds have three mismatches to cynomolgus monkey IRF4.
  • Example 37: Viscosity
  • Viscosity of modified oligonucleotide solutions was measured. The viscocity of 935918 is compatible with weekly subcutaneous injection, and the viscosities of both 935918 and 935968 are compatible with IV dosing.
  • TABLE 191
    Viscosity
    Compound ID Dose (mg/mL) by weight Viscocity (cP)
    690890 300 16.14
    935658 300 48.79
    935696 300 120.2
    935762 300 11.39
    935918 100 2.12
    935968 300 53.76
    882800 100 3.4

Claims (18)

1-65. (canceled)
66. A compound comprising a modified oligonucleotide 10 to 30 linked nucleosides in length having a nucleobase sequence comprising at least 10 contiguous nucleobases of the nucleobase sequence of SEQ ID NO: 2021, or a pharmaceutically acceptable salt thereof.
67. The compound of claim 66, wherein the modified oligonucleotide comprises a nucleobase sequence of SEQ ID NO: 2021.
68. The compound of claim 66, wherein the modified oligonucleotide consists of a nucleobase sequence of SEQ ID NO: 2021.
69. The compound of claim 66, wherein the modified oligonucleotide comprises at least one modified internucleoside linkage, at least one modified sugar, or at least one modified nucleobase.
70. The compound of claim 69, wherein the modified internucleoside linkage is a phosphorothioate internucleoside linkage.
71. The compound of claim 69, wherein the modified sugar is a bicyclic sugar.
72. The compound of claim 69, wherein the bicyclic sugar is selected from the group consisting of: 4′-(CH2)—O-2′ (LNA); 4′-(CH2)2—O-2′ (ENA); and 4′-CH(CH3)—O-2′ (cEt).
73. The compound of claim 69, wherein the modified sugar is 2′-O-methoxyethyl.
74. The compound of claim 69, wherein the modified nucleobase is 5-methylcytosine.
75. The compound of claim 66, wherein the modified oligonucleotide comprises:
a gap segment consisting of linked deoxyribonucleotides;
a 5′ wing segment consisting of linked nucleosides; and
a 3′ wing segment consisting of linked nucleosides;
wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment and wherein each nucleoside of each wing segment comprises a modified sugar.
76. The compound of claim 75, wherein:
the gap segment consists of nine linked deoxynucleosides;
the 5′ wing segment consists of two linked nucleosides; and
the 3′ wing segment consists of five linked nucleosides;
wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of the 5′ wing segment comprises a cEt nucleoside;
wherein the 3′ wing segment comprises a 2′-O-methoxymethyl nucleoside, a 2′-O-methoxymethyl nucleoside, a 2′-O-methoxymethyl nucleoside, a cEt nucleoside, and a cEt nucleoside in the 5′ to 3′ direction; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine.
77. The compound of claim 66, wherein the compound is a sodium salt.
78. A composition comprising the compound of claim 66 and a pharmaceutically acceptable carrier.
79. A method for treating or ameliorating a cancer in an individual comprising administering a composition of claim 78.
80. The method of claim 79, wherein the cancer is a blood cancer, myeloma, multiple myeloma, B cell malignancy, lymphoma, B cell lymphoma, T cell lymphoma, or leukemia.
81. The method of claim 79, wherein the cancer is multiple myeloma.
82. The method of claim 79, wherein the composition is administered parenterally.
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